This lesson introduces the concept of invariant columns and why they should be removed. It also provides a function to remove them.
All of this material will appear on the exam. Take notes on the workflow, functions, and concepts.
By the end of this lesson you will
SNPs are Single Nucleotide Polymorphisms. This means that they are by definition polymorphic - more than one nucleotide occurs in that position (locus) in different individual in a species. For example, most individuals in a population may be G|G, but some are G|A or even A|A.
The SNP concept applies at the level of a species. Within separate populations of a species (or individuals genotyped for a study) only one allele of the SNP may be present. This means that though there is genetic variation at that locus in the level of species, for the the population or sample for a study there is no variation.
If all individuals in a population are homozygous for either the major allele (e.g. all are MM), or all are homozygous for the minor allele (e.g. all are mm) we say that the allele is fixed in that population. They other allele is present in other populations, but not all of them. When an allele is fixed in a population it is actually very useful for distinguishing that population genetically from others.
Similarly, for a sample of individuals in a single study, all individuals genotyped may turn out to be the same type of homozygote for a SNP - all are mm or MM. A different sample may have yield heterozygotes or a mix of both types of homozygotes (mm and MM), but for the data at hand, only one type of homozygote is present. While the allele is not necessarily fixed in any population, it is invariant in the individuals that happened to be gentoyped.
SNP data is converted to numeric genotype scores for analysis with machine learning methods such as PCA. If a SNP is invariant in all of the individuals genotyped in a sample for a study, the entire column (aka feature) in the dataframe will be either 0 (all individuals have the major allele) or 2 (all individuals have the minor allele). Similarly, if all individuals are heterozygotes, the entire column will be 1.
Completely invariant alleles in a dataset present 2 issues:
When a column in a dataset is invariant, whether a SNP or anything else, it doesn’t provide you any useful information. For example, if I want to predict whether taking Advanced Placement (AP) Biology predicts success in my intro biology course, and everyone in the class has taken AP Bio, then I can’t learn or conclude anything.
Invariant features, however, still have to be handled by the computer. They therefore eat up computational resources. Since SNP data can have tens or ever hundreds of thousands of features, this can be a major waste of computational time. It is therefore advisable to remove invariant features to speed up the your analyses.
A feature that is invariant will have a standard deviation of 0. For example:
x <- c(2,2,2,2,2,2)
mean(x)## [1] 2sd(x)## [1] 0While we can calculate the mean and standard deviation of an invariant feature, we can’t scale it because this requires division by 0, which is not defined: there is no answer to, for example, x/0.
More generally, machine learning algorithms can run into problems with invariant features and fail to work. It is therefore advisable to remove invariant features before an analysis.
There are several ways to identify if a column in a dataframe is invariant, but probably the easiest is to calculate the standard deviation. The standard deviation is a measure of variation in the data, and if everything in a column is the same, there is no variation and the sd = 0. You could similarly calculate the range; if all the data in a column is 2, then the minimum is 2, the max is 2, and the range is 2 - 2 = 0.
Here’s some example data that shows that this works for all 3 possible forms of invariant SNP genotypic scores data:
First, some fake data. Add c() to make the vectors.
# add the c() function to make all of the vectors
# All samples are homozygous for major allele
SNP_fixed_0 <- c(0, 0, 0, 0, 0, 0) # TODO
# All samples are homozygous for minor allele
SNP_fixed_2 <- c(2, 2, 2, 2, 2, 2) # TODO
# All samples are heterozygous, e.g "A|G"
SNP_all_hetero <- c(1, 1, 1, 1, 1, 1) # TODONow the standard deviations with sd():
# add sd() to calculate the SDs
sd(SNP_fixed_0) # TODO## [1] 0sd(SNP_fixed_2)## [1] 0sd(SNP_all_hetero)## [1] 0Now let’s make a larger dataframe with some features that aren’t invariant.
First, some invariant features:
# Mixture of the 2 homozygotes
SNP_mix_vs1 <- c(0, 0, 0, 2, 2, 2)
# Mixture of the 2 homozygotes
## and heterozygotes
SNP_mix_vs2 <- c(0, 0, 1, 1, 2, 2)We put these into a dataframe:
# add data.frame() and assign to an object
## called df to look at the data
df<- data.frame(SNP_fixed_0, # TODO
SNP_fixed_2,
SNP_mix_vs1,
SNP_mix_vs2)
df## SNP_fixed_0 SNP_fixed_2 SNP_mix_vs1 SNP_mix_vs2
## 1 0 2 0 0
## 2 0 2 0 0
## 3 0 2 0 1
## 4 0 2 2 1
## 5 0 2 2 2
## 6 0 2 2 2To identify which columns are invariant we first calculate all the SDs.
# add sd() to calculate the SDs
# add [, 1] etc to each line
## lines to calculate the sd on each column
## The first one is shown as an exame
#add [, 1]
sd_col01 <- sd(df[,1]) # EXAMPLE
#add [, 2]
sd_col02 <- sd(df[,2]) # TODO
#add [, 3]
sd_col03 <- sd(df[,3]) # TODO
#add [, 4]
sd_col04 <- sd(df[,4]) # TODOWe can put this all into a vector that contains the SDs:
# add c() to make into a vector
## assign it to a vector called sd_vector
sd_vector<- c(sd_col01, # TODO
sd_col02,
sd_col03,
sd_col04)Now use which() to see which parts of the vector are
equal to 0.
# add which() and == 0
which(sd_vector ==0 ) # TODO## [1] 1 2We’ll save this to a vector to hold the indices of the invariant columns.
# assign to a vector called i_invariant
i_invariant<- which(sd_vector == 0) # TODOThis vector of indices can be used to look at which columns are invariant in our dataframe:
# add [,i_invariant] to see
## the invariant columns
df[,i_invariant] # TODO## SNP_fixed_0 SNP_fixed_2
## 1 0 2
## 2 0 2
## 3 0 2
## 4 0 2
## 5 0 2
## 6 0 2We can then use this to show use which columns DO vary by using negative indexing to remove the invariant columns.
# add -i_invariant to REMOVE the invariant columns
df[,-i_invariant] # TODO## SNP_mix_vs1 SNP_mix_vs2
## 1 0 0
## 2 0 0
## 3 0 1
## 4 2 1
## 5 2 2
## 6 2 2We can then make a new dataframe of just the variant columns
# assign to a dataframe called df03
df03<- df[,-i_invariant] #TODOLook at the results:
df03## SNP_mix_vs1 SNP_mix_vs2
## 1 0 0
## 2 0 0
## 3 0 1
## 4 2 1
## 5 2 2
## 6 2 2The function below will remove invariant columns from a dataframe, as
long as you add return(x) to the end.
# run this function
## add return(x_no_invar)
invar_omit <- function(x){
cat("Dataframe of dim",dim(x), "processed...\n")
sds <- apply(x, 2, sd, na.rm = TRUE)
i_var0 <- which(sds == 0)
cat(length(i_var0),"columns removed\n")
if(length(i_var0) > 0){
x <- x[, -i_var0]
}
## add return() with x in it
return(x) #TODO
}
warning("Reminder: Did you add return() to the function?")## Warning: Reminder: Did you add return() to the function?We can test it on our data above.
# run invar_omit() on df
invar_omit(df) # TODO## Dataframe of dim 6 4 processed...
## 2 columns removed## SNP_mix_vs1 SNP_mix_vs2
## 1 0 0
## 2 0 0
## 3 0 1
## 4 2 1
## 5 2 2
## 6 2 2It should only change data dataframe when columns are invariant. Its always good to test a function to make sure it does what you want. If we run it once, save the output, and run it again on the output we just made, it shouldn’t remove anything the second time.
# run invar_omit() on df
df_no_invar <- invar_omit(df) # TODO## Dataframe of dim 6 4 processed...
## 2 columns removed# look out output
df_no_invar## SNP_mix_vs1 SNP_mix_vs2
## 1 0 0
## 2 0 0
## 3 0 1
## 4 2 1
## 5 2 2
## 6 2 2# run invar_omit() on df_no_invar
(df_no_invar) # TODO## SNP_mix_vs1 SNP_mix_vs2
## 1 0 0
## 2 0 0
## 3 0 1
## 4 2 1
## 5 2 2
## 6 2 2Let’s work through an example with a real VCF file. The steps we need to follow are
vcfR package..vcffile is present with
list.files()vcfR::read.vcfR()vcfR::extract.gt()t()invar_omit()First, load up the vcfR package with library() and check
the working directory with getwd().
# call library() on vcfR
library(vcfR) #TODO##
## ***** *** vcfR *** *****
## This is vcfR 1.13.0
## browseVignettes('vcfR') # Documentation
## citation('vcfR') # Citation
## ***** ***** ***** *****# check your working directory with getwd()
getwd() #TODO## [1] "/Users/krishna/Downloads"Second, set the working directory to the location of this file if it isn’t already. Do this via
Session->Set Working Directory -> To source file location
Third, make sure the file all_loci.vcf is present with
list.files() and/or
list.files(pattern = "vcf").
list.files()## [1] " Post lab 3 B.pdf"
## [2] "[16133722 - HUMOR] The Princess Bride and the parodic impulse_ The seduction of Cinderella (1).pdf"
## [3] "[16133722 - HUMOR] The Princess Bride and the parodic impulse_ The seduction of Cinderella (2).pdf"
## [4] "[16133722 - HUMOR] The Princess Bride and the parodic impulse_ The seduction of Cinderella (3).pdf"
## [5] "[16133722 - HUMOR] The Princess Bride and the parodic impulse_ The seduction of Cinderella.pdf"
## [6] "{7C8D6B82-D416-40FB-BA89-80783DECEA3B}.png.jpg"
## [7] "~$iman CH 4 & Conclusion.doc"
## [8] "~$Lab Meeting 2 Daphnia Excel sheet 3.25.21.xlsx"
## [9] "~$ligon and science final .docx"
## [10] "~$liogn and science paper.docx"
## [11] "~$TRODUCTION TO AFRICA -- FINAL PAPER OUTLINES (2).docx"
## [12] "~$TRODUCTION TO AFRICA -- FINAL PAPER OUTLINES.docx"
## [13] "~$TRODUCTION TO AFRICA -- LECTURE NOTES - 2-5 (2).docx"
## [14] "~$wilding Discussion Questions-4.docx"
## [15] "0110 F20 Recitation Worksheet 2 Send (1).pdf"
## [16] "0110 F20 Recitation Worksheet 2 Send.pdf"
## [17] "0110 F20 420 PM Syllabus Updated with Canvas Compliance (1).pdf"
## [18] "0110 F20 420 PM Syllabus Updated with Canvas Compliance (2).pdf"
## [19] "0110 F20 420 PM Syllabus Updated with Canvas Compliance (3).pdf"
## [20] "0110 F20 420 PM Syllabus Updated with Canvas Compliance (4).pdf"
## [21] "0110 F20 420 PM Syllabus Updated with Canvas Compliance (5).pdf"
## [22] "0110 F20 420 PM Syllabus Updated with Canvas Compliance (6).pdf"
## [23] "0110 F20 420 PM Syllabus Updated with Canvas Compliance (7).pdf"
## [24] "0110 F20 420 PM Syllabus Updated with Canvas Compliance (8).pdf"
## [25] "0110 F20 420 PM Syllabus Updated with Canvas Compliance.pdf"
## [26] "0110 F20 Openstax Practice Exercises.pdf"
## [27] "0110 F20 Openstax Practice Questions Chapter 6 Electronic Structure and Periodic Properties of Elements.pdf"
## [28] "0110 F20 Outline of Possible Final Exam Material.pdf"
## [29] "0110 F20 Recitation Skills Inventory for Students Send.pdf"
## [30] "0110 F20 Recitation Worksheet 1 For Students (1).pdf"
## [31] "0110 F20 Recitation Worksheet 1 For Students (2).pdf"
## [32] "0110 F20 Recitation Worksheet 1 For Students (3).pdf"
## [33] "0110 F20 Recitation Worksheet 1 For Students.pdf"
## [34] "0110 F20 Recitation Worksheet 2 Key Send.pdf"
## [35] "0110 F20 Rules for Drawing Lewis Structures Post on Canvas.pdf"
## [36] "0110 F20 Schedule Post.pdf"
## [37] "0110 F20 Schedule Updated Post (1).pdf"
## [38] "0110 F20 Schedule Updated Post (10).pdf"
## [39] "0110 F20 Schedule Updated Post (11).pdf"
## [40] "0110 F20 Schedule Updated Post (12).pdf"
## [41] "0110 F20 Schedule Updated Post (13).pdf"
## [42] "0110 F20 Schedule Updated Post (14).pdf"
## [43] "0110 F20 Schedule Updated Post (15).pdf"
## [44] "0110 F20 Schedule Updated Post (16).pdf"
## [45] "0110 F20 Schedule Updated Post (17).pdf"
## [46] "0110 F20 Schedule Updated Post (2).pdf"
## [47] "0110 F20 Schedule Updated Post (3).pdf"
## [48] "0110 F20 Schedule Updated Post (4).pdf"
## [49] "0110 F20 Schedule Updated Post (5).pdf"
## [50] "0110 F20 Schedule Updated Post (6).pdf"
## [51] "0110 F20 Schedule Updated Post (7).pdf"
## [52] "0110 F20 Schedule Updated Post (8).pdf"
## [53] "0110 F20 Schedule Updated Post (9).pdf"
## [54] "0110 F20 Schedule Updated Post.pdf"
## [55] "0120 SP21 Notes for Students February 15 Post.pdf"
## [56] "0120 SP21 Openstax Chapter 11 Lecture Notes for Students February 5.pdf"
## [57] "0120 SP21 Recitation Worksheet 1 Chapter 10 for Students.pdf"
## [58] "0120_SP21_Recitation_Worksheet_Gradescope_Template_for_Week_of_February_14.pdf"
## [59] "0120_SP21_Recitation_Worksheet_March_29.pdf"
## [60] "0120+SP21+Recitation+Worksheet+1+Chapter+10+for+Students.pdf"
## [61] "1 0110 F20 Open Stax Chapter 1 Objectives.pdf"
## [62] "1.1 FINAL.pdf"
## [63] "10.1007_s10646-013-1061-1.ris"
## [64] "1189983.vcf"
## [65] "125938668.pdf"
## [66] "13_FABRIZIO PREGADIO_The_Way_of_the_Golden_Elixir.pdf"
## [67] "14_vivienne Lo_Food and Medicine in Traditional China.pdf"
## [68] "1540_cluster_analysis.pdf"
## [69] "1597512097.031946.jpg"
## [70] "1651137.acsm"
## [71] "2211.HAA.0010-1.Schedule.Final.docx"
## [72] "2211.HAA.0010.Handout-Power&Authority-Benin.pdf"
## [73] "2211.Handout-Descent.Bosch (1).pdf"
## [74] "2211.Handout-Descent.Bosch (2).pdf"
## [75] "2211.Handout-Descent.Bosch .pdf"
## [76] "2211.Handout-Hongzhi.Velazquez (1).docx"
## [77] "2211.Handout-Hongzhi.Velazquez.docx"
## [78] "2211.Handout-Li Cheng.Sotatsu.Hokusai.pdf"
## [79] "2211.Handout-Mosque.Cordoba.pdf"
## [80] "2211.Handout-Parthenon-1.pdf"
## [81] "2211.Handout-Rome.Forbidden.City.docx"
## [82] "2211.Handout.Power&Authority-Trajan.Bayeux (1).pdf"
## [83] "2211.Handout.Power&Authority-Trajan.Bayeux.pdf"
## [84] "2211.Smithson.Christo & Jeanne-Claude (1).pdf"
## [85] "2211.Smithson.Christo & Jeanne-Claude (2).pdf"
## [86] "2211.Smithson.Christo & Jeanne-Claude.pdf"
## [87] "2221_Exam3.pdf"
## [88] "3_The Meaning of “Culture” _ The New Yorker.pdf"
## [89] "3.Moai.Figures.and.VVM (1).pdf"
## [90] "3.Moai.Figures.and.VVM (2).pdf"
## [91] "3.Moai.Figures.and.VVM.pdf"
## [92] "5_Sun, Anna_Confucianism as a World Religion 2013.pdf"
## [93] "6.pdf"
## [94] "64875390710__ADFCE9EB-FF11-43DF-9002-B9A963EFA982.heic"
## [95] "824f8f2a5d6dbc6ad05b8beb5c3f3a30.torrent"
## [96] "A Pictorial Tour of Garfield Community Farm (1).pdf"
## [97] "A Pictorial Tour of Garfield Community Farm (2).pdf"
## [98] "A Pictorial Tour of Garfield Community Farm.pdf"
## [99] "A Pocket Style Manual 6th Editon by Hacker, Diana Sommers, Nancy (z-lib.org).pdf"
## [100] "A704A49F-15C5-4CCC-B85A-026D3DD079C6.jpg"
## [101] "Academic Foundations assignment.pdf"
## [102] "ACFrOgBpCSeTqGyNLw04rSSauwQg1tZ2TeQXf9JBPwhiZmA9EXu-aj8jdHkkVnu_2kOxNcB9WmOqufxFiBLctXdNWV6QmDYXz_kneq0QZgDAEkK89sruDsoBhXeqil630sHH19A7IZxzyAFlvzwg.pdf"
## [103] "AcroRdrDC_2100120145_MUI.dmg"
## [104] "AcroRdrDC_2100120145_MUI.pkg"
## [105] "Activity 2 In-Lab Workshop Problems, Part 1 and Part 2 (for printing if desired).pdf"
## [106] "Activity 2 Watson and Crick original paper.pdf"
## [107] "Africa_Fourth_Edition_----_(2._Legacies_of_the_Past_Themes_in_African_History).pdf"
## [108] "alcoholedu-for-college-part-two.pdf"
## [109] "all_loci-1.vcf"
## [110] "all_loci.vcf"
## [111] "ALL.chr10_GRCh38.genotypes.20170504.vcf.gz"
## [112] "allomtery_3_scatterplot3d (1).Rmd"
## [113] "Analyze_Course-wide_Community_data-1.pptx"
## [114] "anki-2.1.32-mac.dmg"
## [115] "annotated-Beetleguese%20essay.docx.pdf"
## [116] "annotated-Libraynth%20.pdf"
## [117] "annotated-Reflections%20Religion%20and%20Science (1).pdf"
## [118] "annotated-Reflections%20Religion%20and%20Science.pdf"
## [119] "Answer Key_Chem 0310_Study guide_FInal exam_Fall 2021.pdf"
## [120] "Anthro Mini Presentation (1).pdf"
## [121] "Anthro Mini Presentation.pdf"
## [122] "AP Chapter 14 Jeopardy.ppt"
## [123] "Appa.jpg"
## [124] "Aristotle-1.Physics (1).pdf"
## [125] "Aristotle-1.Physics (2).pdf"
## [126] "Aristotle-1.Physics (3).pdf"
## [127] "Aristotle-1.Physics.pdf"
## [128] "Art Final - Google Docs (1).pdf"
## [129] "Art Final - Google Docs (2).pdf"
## [130] "Art Final - Google Docs (3).pdf"
## [131] "Art Final - Google Docs (4).pdf"
## [132] "Art Final - Google Docs.pdf"
## [133] "Art final part 2 - Google Docs.pdf"
## [134] "Assistant Coordinator Final Schedule.xlsx"
## [135] "Auto Ethnographic Assignment #1 – Language.pdf"
## [136] "Avatar.jpg"
## [137] "Back to the Basics of Ecology-Carson (1).pptx"
## [138] "Back to the Basics of Ecology-Carson (2).pptx"
## [139] "Back to the Basics of Ecology-Carson.pptx"
## [140] "Bakar_Science_and_Religion_Christian_and_Muslim_Perspectives.AlGhazali and Averroes (1).pdf"
## [141] "Bakar_Science_and_Religion_Christian_and_Muslim_Perspectives.AlGhazali and Averroes (2).pdf"
## [142] "Bakar_Science_and_Religion_Christian_and_Muslim_Perspectives.AlGhazali and Averroes.pdf"
## [143] "Beetleguese essay.docx"
## [144] "Beetleguese essay.pdf"
## [145] "Bibliography_679d7d3b-9152-4b12-a5d9-29a809ab19a7.docx"
## [146] "Bio lab week 12 (1).pdf"
## [147] "Bio lab week 12.docx"
## [148] "Bio lab week 12.pdf"
## [149] "bio office hours.docx"
## [150] "BIOSC 0150 (2211) - Course Schedule_FINAL (1).pdf"
## [151] "BIOSC 0150 (2211) - Course Schedule_FINAL.pdf"
## [152] "BIOSC 0150 (2211) - Quiz Wrapper.docx"
## [153] "BIOSC 0150 (2211) - Syllabus_FINAL (1).pdf"
## [154] "BIOSC 0150 (2211) - Syllabus_FINAL.pdf"
## [155] "BIOSC 0150 Grade Calculator (final).xlsx"
## [156] "BIOSC 0150 Module 1_ Biomolecules (1).apkg"
## [157] "BIOSC 0150 Module 1_ Biomolecules (2).apkg"
## [158] "BIOSC 0150 Module 1_ Biomolecules (3).apkg"
## [159] "BIOSC 0150 Module 1_ Biomolecules (4).apkg"
## [160] "BIOSC 0150 Module 1_ Biomolecules (5).apkg"
## [161] "BIOSC 0150 Module 1_ Biomolecules (6).apkg"
## [162] "BIOSC 0150 Module 1_ Biomolecules (7).apkg"
## [163] "BIOSC 0150 Module 1_ Biomolecules.apkg"
## [164] "Black_Bodies_White_Gazes_The_Continuing_Significance_of_Race_in_America.pdf"
## [165] "Blog #3 (1).docx"
## [166] "Blog #3.docx"
## [167] "Blog Entry 2 (1).docx"
## [168] "Blog Entry 2.docx"
## [169] "Blog number 1 Bio lab (1).docx"
## [170] "Blog number 1 Bio lab (2).docx"
## [171] "Blog number 1 Bio lab.docx"
## [172] "Body Fat.mpx"
## [173] "brockstring_SPSS_04October_JG.sav"
## [174] "Brodd_Ch 1_Religion.pdf"
## [175] "Bullshit.pdf"
## [176] "c0110_expt1_intro.pdf"
## [177] "c0110_expt1_online (1).pdf"
## [178] "c0110_expt1_online.pdf"
## [179] "c0110_expt11_intro.pdf"
## [180] "c0110_expt11_online_fillable_pdf (1).pdf"
## [181] "c0110_expt11_online_fillable_pdf.pdf"
## [182] "c0110_expt2_intro.pdf"
## [183] "c0110_expt2_online (1) (1).pdf"
## [184] "c0110_expt2_online (1) (2).pdf"
## [185] "c0110_expt2_online (1).pdf"
## [186] "c0110_expt2_online.pdf"
## [187] "c0110_expt3_intro.pdf"
## [188] "c0110_expt3_online (1).pdf"
## [189] "c0110_expt3_online (2).pdf"
## [190] "c0110_expt3_online (3).pdf"
## [191] "c0110_expt3_online.pdf"
## [192] "c0110_expt4_intro (1).pdf"
## [193] "c0110_expt4_intro (2).pdf"
## [194] "c0110_expt4_intro (3).pdf"
## [195] "c0110_expt4_intro.pdf"
## [196] "c0110_expt4_online (1).pdf"
## [197] "c0110_expt4_online.pdf"
## [198] "c0110_expt5_intro (1).pdf"
## [199] "c0110_expt5_intro.pdf"
## [200] "c0110_expt5_online_fillable (1).pdf"
## [201] "c0110_expt5_online_fillable.pdf"
## [202] "c0110_expt6_intro (1).pdf"
## [203] "c0110_expt6_intro.pdf"
## [204] "c0110_expt6_online_fillable (1).pdf"
## [205] "c0110_expt6_online_fillable (2) (1).pdf"
## [206] "c0110_expt6_online_fillable (2).pdf"
## [207] "c0110_expt6_online_fillable.pdf"
## [208] "c0110_expt7_online_fillable_pdf.pdf"
## [209] "c0110_expt7Iintro.pdf"
## [210] "c0110_expt8_online_fillable_pdf.pdf"
## [211] "c0110_expt9_online_fillable_pdf.pdf"
## [212] "c0120_expt1.pdf"
## [213] "c0120_expt10_online_fillable.pdf"
## [214] "c0120_expt2_chromatograms.pdf"
## [215] "c0120_expt2_intro.pdf"
## [216] "c0120_expt3_online_fillable.pdf"
## [217] "c0120_expt8_online_fillable.pdf"
## [218] "c0120_expt9_online_fillable.pdf"
## [219] "CAC.png"
## [220] "Calendar.pdf"
## [221] "Campbell pp 19-31.pdf"
## [222] "Campbell pp 210-211.pdf"
## [223] "Carson and Root 2000 copy.pdf"
## [224] "Carson et al. post release APIS2008(2) (1).pdf"
## [225] "Carson et al. post release APIS2008(2) (2).pdf"
## [226] "Carson et al. post release APIS2008(2).pdf"
## [227] "center_function (1).R"
## [228] "center_function.R"
## [229] "Ch 13 Study Guide.pdf"
## [230] "Ch 14 Study Guide.pdf"
## [231] "Ch 7 lecture 1.pdf"
## [232] "Ch4 Getting wasted .doc"
## [233] "Ch5 getting wasted.doc"
## [234] "Ch6 getting wasted.doc"
## [235] "Chan paper (1).pdf"
## [236] "Chan paper (2).pdf"
## [237] "Chan paper (3).pdf"
## [238] "Chan paper (4).pdf"
## [239] "Chan paper (5).pdf"
## [240] "Chan paper (6).pdf"
## [241] "Chan paper.pdf"
## [242] "Chapter 21 Study Guide.pdf"
## [243] "Chapter 22 Study Guide.pdf"
## [244] "Chapter 55 study guide.pdf"
## [245] "ChartReviewInformation_Clinica (1).pdf"
## [246] "ChartReviewInformation_Clinica (2).pdf"
## [247] "ChartReviewInformation_Clinica.pdf"
## [248] "Chem 0310_Fall 2021_Chapter 3.pdf"
## [249] "Chem 0310_Feel Good Exam_Fall 2021.docx"
## [250] "Chem 0310_Study guide_FInal exam_Fall 2021.pdf"
## [251] "Chem 0310_Take Home Exam_Fall 2021 (1).pdf"
## [252] "Chem 0310_Take Home Exam_Fall 2021.pdf"
## [253] "Chem 2 Lab 1 (1).pdf"
## [254] "Chem 2 Lab 1 (2).pdf"
## [255] "Chem 2 Lab 1.pdf"
## [256] "Chem 2 Lab 2.pdf"
## [257] "Chem+0310_Feel+Good+Exam_Fall+2021.pdf"
## [258] "Chem+0310_Take+Home+Exam_Fall+2021-1.pdf"
## [259] "Chem+0310_Take+Home+Exam_Fall+2021.pdf"
## [260] "CHEM0310_Problem Set 2_Fall 2021.pdf"
## [261] "CHEM0310_Problem Set 3_Fall 2021 (1).pdf"
## [262] "CHEM0310_Problem Set 3_Fall 2021.pdf"
## [263] "CHEM0310_Problem Set 7_Fall 2021.pdf"
## [264] "CHEM0310_Problem Set 9_Fall 2021.pdf"
## [265] "Chemically Active Extraction (Slides).pdf"
## [266] "Chemistry2e textbook.pdf"
## [267] "CLARK - PHYS 0212-0219 - Lecture 01 - Changing Motion.pdf"
## [268] "ClinicalOutcomesFollowingRotat_2020-10-16_1156.pdf"
## [269] "ClinicalOutcomesFollowingRotat_2020-10-28_1331.pdf"
## [270] "ClinicalOutcomesFollowingRotat_2020-10-28_1343.pdf"
## [271] "ClinicalOutcomesFollowingRotat_2020-10-28_1344.pdf"
## [272] "ClinicalOutcomesFollowingRotat_2020-10-28_1348.pdf"
## [273] "ClinicalOutcomesFollowingRotat_2020-10-30_1842.pdf"
## [274] "ClinicalOutcomesFollowingRotat_2020-11-30_1230.pdf"
## [275] "ClinicalOutcomesFollowingRotat_2020-12-02_1503.pdf"
## [276] "ClinicalOutcomesFollowingRotat_DataDictionary_2020-10-16.csv"
## [277] "ClinicalOutcomesFollowingRotat_DataDictionary_2020-10-28 (1).csv"
## [278] "ClinicalOutcomesFollowingRotat_DataDictionary_2020-10-28.csv"
## [279] "ClinicalOutcomesFollowingRotat_DataDictionary_2020-10-30 (1).csv"
## [280] "ClinicalOutcomesFollowingRotat_DataDictionary_2020-10-30.csv"
## [281] "cluster_analysis_portfolio (1).Rmd"
## [282] "cluster_analysis_portfolio.Rmd"
## [283] "cluster_analysis_with_Higgs_aa (1).R"
## [284] "cluster_analysis_with_Higgs_aa.R"
## [285] "cobi.12738 (1).pdf"
## [286] "cobi.12738.pdf"
## [287] "code_checkpoint_vcfR.html"
## [288] "code_checkpoint_vcfR.Rmd"
## [289] "CODE_CHECKPOINT-first_rstudio_script (1).R"
## [290] "CODE_CHECKPOINT-first_rstudio_script (2).R"
## [291] "CODE_CHECKPOINT-first_rstudio_script.R"
## [292] "codon chart (1).png"
## [293] "codon chart.png"
## [294] "Collab_Writing_PEER_REVIEW_WORKSHEET.doc.pdf"
## [295] "CollegeVsHSWriting.pdf"
## [296] "Community slides.pptx"
## [297] "Comp bio shit "
## [298] "Competition-I&II 2014.pptx"
## [299] "Coogan Genesis-1.pdf"
## [300] "Copy of Chapter 13 Textbook Notes.pdf"
## [301] "Corrigan--Writing-About-Film Ch 1 (1).pdf"
## [302] "Corrigan--Writing-About-Film Ch 1 (2).pdf"
## [303] "Corrigan--Writing-About-Film Ch 1.pdf"
## [304] "Corrigan--Writing-About-Film Ch 2.pdf"
## [305] "corriganchapter3-1 (1).pdf"
## [306] "corriganchapter3-1 (2).pdf"
## [307] "corriganchapter3-1 (3).pdf"
## [308] "corriganchapter3-1 (4).pdf"
## [309] "corriganchapter3-1.pdf"
## [310] "Cover Letter Revision Seminar in comp film.docx"
## [311] "Cover Letter Revision Seminar in comp film.pdf"
## [312] "Covid test conformation.pdf"
## [313] "Criminal Justice Intro(1).docx"
## [314] "Cultural_anthropology.pdf"
## [315] "Daphnia thing.xlsx"
## [316] "Daphnia.pptx"
## [317] "data_structures-DFs (1).pdf"
## [318] "data_structures-DFs (2).pdf"
## [319] "data_structures-DFs (3).pdf"
## [320] "data_structures-DFs.pdf"
## [321] "dawkins_science discredits religion.pdf"
## [322] "DBF61B98-02E0-46E1-AF26-E65EF06BC312.jpg"
## [323] "Dennis_social_darwinism_scientific_racism.pdf"
## [324] "Development Theories Primer (1) (1).doc"
## [325] "Development Theories Primer (1).doc"
## [326] "Devils Gardens.pdf"
## [327] "Diagloues .pdf"
## [328] "Diet (1).mpx"
## [329] "Diet.mpx"
## [330] "Discord (1).dmg"
## [331] "Done Teme.pdf"
## [332] "Donlan et al. 2005(4).pdf"
## [333] "download.pdf"
## [334] "eckl,+JNS_23_Amupanda (1).pdf"
## [335] "eckl,+JNS_23_Amupanda.pdf"
## [336] "Ecology - The Economy of Nature 8e [Rick Relyea].pdf"
## [337] "Ecology note card.pdf"
## [338] "Enns evolution of adam ch. 3-1.pdf"
## [339] "ENUMA ELISH.pdf"
## [340] "environmental racism.pdf"
## [341] "Estes_etal_2011 (1).pdf"
## [342] "Evolution and Adaptation, Life Histories-Carson-6.pptx"
## [343] "Exam 1_ Krishna Patel_files"
## [344] "Exam 1_ Krishna Patel.htm"
## [345] "Exam 1_ Krishna Patel.mhtml"
## [346] "Exam 3note cars.pdf"
## [347] "Exam 4 Review Sheet -1.pdf"
## [348] "Exam 4 Review Sheet .pdf"
## [349] "Exam I Practice Questions.pdf"
## [350] "Exam+Ch.+1-6.pdf"
## [351] "Exam+Ch.+7-11.pdf"
## [352] "Exam3_2204.pdf"
## [353] "Exam3am_2191.pdf"
## [354] "Example Exam 3 Questions.pdf"
## [355] "Example Exam Questions (1).pdf"
## [356] "Example Exam Questions (2).pdf"
## [357] "Example Exam Questions.pdf"
## [358] "Exp 1 - GC2.pdf"
## [359] "Experiment 10 Chem 1 Lab.pdf"
## [360] "Experiment 12.pdf"
## [361] "Expermient 11.pdf"
## [362] "Fantasy Brewer pg 193 (1).pdf"
## [363] "Fantasy Brewer pg 193 (2).pdf"
## [364] "Fantasy Brewer pg 193.pdf"
## [365] "feature_engineering (1).Rmd"
## [366] "feature_engineering_intro_2_functions-part2.Rmd"
## [367] "feature_engineering.Rmd"
## [368] "feb28.pdf"
## [369] "fiji-macosx.zip"
## [370] "file (1).pdf"
## [371] "file.pdf"
## [372] "Film Terms Sheets.pdf"
## [373] "final exam review burlew.pptx"
## [374] "Final_Exam_Formula_Sheet (1).pdf"
## [375] "Final_Exam_Formula_Sheet (2).pdf"
## [376] "Final_Exam_Formula_Sheet.pdf"
## [377] "Flaming Snowball - Gabrielle & Lisa (1).doc"
## [378] "Flaming Snowball - Gabrielle & Lisa.doc"
## [379] "Flex Pitt Provisions.pdf"
## [380] "Flow Chart.pdf"
## [381] "Forest Dynamics talk (1).pptx"
## [382] "Forest Dynamics talk (2).pptx"
## [383] "Forest Dynamics talk .pptx"
## [384] "free jazz.pdf"
## [385] "Freshman year Pitt"
## [386] "Freud Dreams pp 34-44 (1).pdf"
## [387] "Freud Dreams pp 34-44 (2).pdf"
## [388] "Freud Dreams pp 34-44.pdf"
## [389] "Freud Uncanny (1).pdf"
## [390] "Freud Uncanny.pdf"
## [391] "Furhter direction sldie.pptx"
## [392] "Galileo Galilei_Letter to Grand Duchess.pdf"
## [393] "Galileo Goes to Jail_ And Other Myths about Science and Religion.pdf"
## [394] "Galileo_Starry Messenger.pdf"
## [395] "Garfield Farms Essay.docx"
## [396] "GCB lecture 11-18-2021 (1).pptx"
## [397] "GCB lecture 11-18-2021 (2).pptx"
## [398] "GCB lecture 11-18-2021 (3).pptx"
## [399] "GCB lecture 11-18-2021.pptx"
## [400] "Genesis Rabbah.pdf"
## [401] "Getting Wasted Soc Ch.2-3.doc"
## [402] "Getting Wasted Soc Ch1.doc"
## [403] "Giberson Chap 3 (1).pdf"
## [404] "Giberson Chap 3.pdf"
## [405] "glassware_specs.pdf"
## [406] "Global Citizenship.png"
## [407] "Goldberg_Genetics_7e_CH09_SMSG_pdf (1).pdf"
## [408] "Goldberg_Genetics_7e_CH09_SMSG_pdf.pdf"
## [409] "Goldberg_Genetics_7e_CH12_SMSG_pdf.pdf"
## [410] "Gould.Two Separate Domains.pdf"
## [411] "Group Assignment (1).pdf"
## [412] "Group Assignment.pdf"
## [413] "guest lecture seed banks (1).pptx"
## [414] "guest lecture seed banks.pptx"
## [415] "HAA 0010 FINAL PROJECT COMPARATIVE ANALYSIS RUBRIC (1).docx"
## [416] "HAA 0010 FINAL PROJECT COMPARATIVE ANALYSIS RUBRIC.docx"
## [417] "Handout #1_ What is Art_"
## [418] "Handout 1 (Accompanying Slides).pdf"
## [419] "Handout 10 (Accompanying Slides) (1).pdf"
## [420] "Handout 10 (Accompanying Slides).pdf"
## [421] "Handout 11 (Accompanying Slides) (1).pdf"
## [422] "Handout 11 (Accompanying Slides).pdf"
## [423] "Handout 12 (Accompanying Slides).pdf"
## [424] "Handout 13 (Accompanying Slides).pdf"
## [425] "Handout 14 (Accompanying Slides) (1).pdf"
## [426] "Handout 14 (Accompanying Slides) (2).pdf"
## [427] "Handout 14 (Accompanying Slides).pdf"
## [428] "Handout 15 (Accompanying Slides) (1).pdf"
## [429] "Handout 15 (Accompanying Slides) (2).pdf"
## [430] "Handout 15 (Accompanying Slides).pdf"
## [431] "Handout 16 (Accompanying Slides).pdf"
## [432] "Handout 17 (Accompanying Slides).pdf"
## [433] "Handout 18 (Accompanying Slides).pdf"
## [434] "Handout 19 (Accompanying Slides).pdf"
## [435] "Handout 2(Accompanying Slides).pdf.pdf"
## [436] "Handout 20 (Accompanying Slides).pdf"
## [437] "Handout 3 (Accompanying Slides).pdf"
## [438] "Handout 4 (Accompanying Sldes).pdf"
## [439] "Handout 5 (Accompanying Slides) (1).pdf"
## [440] "Handout 5 (Accompanying Slides).pdf"
## [441] "Handout 6 (Accompanying Slides).pdf"
## [442] "Handout 7 (Accompanying Slides) (1).pdf"
## [443] "Handout 7 (Accompanying Slides) (2).pdf"
## [444] "Handout 7 (Accompanying Slides) (3).pdf"
## [445] "Handout 7 (Accompanying Slides).pdf"
## [446] "Handout 8 (Accompanying Slides) (1).pdf"
## [447] "Handout 8 (Accompanying Slides).pdf"
## [448] "Handout 9 (Accompanying Slides) (1).pdf"
## [449] "Handout 9 (Accompanying Slides).pdf"
## [450] "Hatfull Spencer paper (1).pdf"
## [451] "Hatfull Spencer paper.pdf"
## [452] "Hegazy, Habiel, and Fawzy. 2009 (1).pdf"
## [453] "Hegazy, Habiel, and Fawzy. 2009 (2).pdf"
## [454] "Hegazy, Habiel, and Fawzy. 2009.pdf"
## [455] "HighSchool resume (1).docx"
## [456] "HighSchool resume.docx"
## [457] "Hirsch_etal_2014 (1).pdf"
## [458] "Hirsch_etal_2014 (2).pdf"
## [459] "Hirsch_etal_2014.pdf"
## [460] "Hist.docx"
## [461] "Hist.pdf"
## [462] "HOJ F22 Week 11 hard bop.pdf"
## [463] "HOJ F22 Week 12 free jazz.pdf"
## [464] "HOJ F22 Week 12 racial politics_free jazz 1.pdf"
## [465] "HOJ F22 Week 4 Blues Legacies 1.pdf"
## [466] "HOJ F22 Week 4 New Orleans 1.pdf"
## [467] "HOJ F22 Week 5 Chicago.pdf"
## [468] "HOJ F22 Week 6 Kansas City.pdf"
## [469] "Homework 1 Chapter 1,2,3 (1).pdf"
## [470] "Homework 1 Chapter 1,2,3 (2) (1).pdf"
## [471] "Homework 1 Chapter 1,2,3 (2) (2).pdf"
## [472] "Homework 1 Chapter 1,2,3 (2).pdf"
## [473] "Homework 1 Chapter 1,2,3.pdf"
## [474] "Homework week 8 bio lab.pptx"
## [475] "How to do Mendel type problems (1).pptx"
## [476] "How to do Mendel type problems.pptx"
## [477] "HW-4-5 (1).pdf"
## [478] "HW-4-5.pdf"
## [479] "HW-6.pdf"
## [480] "HW-7-8.pdf"
## [481] "HW+11.pdf"
## [482] "HW+16.pdf"
## [483] "hw16_1_Q3.jpg"
## [484] "id.pdf"
## [485] "IMG_0115.PNG"
## [486] "IMG_0135.PNG"
## [487] "IMG_0237.PNG"
## [488] "IMG_0289 2.HEIC"
## [489] "IMG_0289.HEIC"
## [490] "IMG_0342.HEIC"
## [491] "IMG_0452.HEIC"
## [492] "IMG_0488.JPG"
## [493] "IMG_0762.mov"
## [494] "IMG_0766.mov"
## [495] "IMG_0767.mov"
## [496] "IMG_0769.mov"
## [497] "IMG_0771.mov"
## [498] "IMG_0D9ABA74D56F-1.heic"
## [499] "IMG_2293.HEIC"
## [500] "IMG_2380 copy.jpg"
## [501] "IMG_2380.HEIC"
## [502] "IMG_2393 copy.jpg"
## [503] "IMG_2583.HEIC"
## [504] "IMG_2583.png"
## [505] "IMG_2C431C072954-1.jpeg"
## [506] "IMG_2C431C072954-1.png"
## [507] "IMG_3455.heic"
## [508] "IMG_4440 copy.jpg"
## [509] "IMG_5436 copy.pdf"
## [510] "IMG_6142.heic"
## [511] "IMG_7509 2.HEIC"
## [512] "IMG_8511.heic"
## [513] "IMG_AB9A219EFA7A-1.jpeg"
## [514] "IMG_AB9A219EFA7A-1.png"
## [515] "IMG_B68DD95C6828-1.jpeg"
## [516] "IMG_FDB33BB32CC7-1.jpeg"
## [517] "IMG_FDB33BB32CC7-1.png"
## [518] "individual_notebook_population_spreadsheet_sp21 (1).xlsx"
## [519] "individual_notebook_population_spreadsheet_sp21.xlsx"
## [520] "Install Spotify.app"
## [521] "InstallBackupAndSync.dmg"
## [522] "InstallLDBPackage64c-2-0-8-01.zip"
## [523] "Intro to Africa Final.pdf"
## [524] "Intro to Africa Unit 2 notes.docx"
## [525] "Introduction slides-1-1 (1).pptx"
## [526] "Introduction slides-1-1 (2).pptx"
## [527] "Introduction slides-1-1.pptx"
## [528] "Introduction slides-1.pptx"
## [529] "INTRODUCTION TO AFRICA - FILMS {SAHARA, SAVANNA, FOREST} (1).docx"
## [530] "INTRODUCTION TO AFRICA - FILMS {SAHARA, SAVANNA, FOREST}.docx"
## [531] "INTRODUCTION TO AFRICA - TEST GUIDELINES - 2 (1).docx"
## [532] "INTRODUCTION TO AFRICA - TEST GUIDELINES - 2-1.docx"
## [533] "INTRODUCTION TO AFRICA - TEST GUIDELINES - 2.docx"
## [534] "INTRODUCTION TO AFRICA - TEST GUIDELINES (1).docx"
## [535] "INTRODUCTION TO AFRICA - TEST GUIDELINES.docx"
## [536] "INTRODUCTION TO AFRICA -- FINAL PAPER OUTLINES (1).docx"
## [537] "INTRODUCTION TO AFRICA -- FINAL PAPER OUTLINES (2).docx"
## [538] "INTRODUCTION TO AFRICA -- FINAL PAPER OUTLINES.docx"
## [539] "INTRODUCTION TO AFRICA -- LECTURE NOTES - 2 (1).docx"
## [540] "INTRODUCTION TO AFRICA -- LECTURE NOTES - 2-0a8505b7-1bc9-4f6d-99f9-e13dc3ef2ee6.docx"
## [541] "INTRODUCTION TO AFRICA -- LECTURE NOTES - 2-11df78e7-773b-4443-96ba-d7a319003b76.docx"
## [542] "INTRODUCTION TO AFRICA -- LECTURE NOTES - 2-2.docx"
## [543] "INTRODUCTION TO AFRICA -- LECTURE NOTES - 2-3.docx"
## [544] "INTRODUCTION TO AFRICA -- LECTURE NOTES - 2-5 (1).docx"
## [545] "INTRODUCTION TO AFRICA -- LECTURE NOTES - 2-5 (2).docx"
## [546] "INTRODUCTION TO AFRICA -- LECTURE NOTES - 2-5.docx"
## [547] "INTRODUCTION TO AFRICA -- LECTURE NOTES - 2-6 (1).docx"
## [548] "INTRODUCTION TO AFRICA -- LECTURE NOTES - 2-6.docx"
## [549] "INTRODUCTION TO AFRICA -- LECTURE NOTES - 2-7.docx"
## [550] "INTRODUCTION TO AFRICA -- LECTURE NOTES - 2-ed609f97-4368-4e02-94c0-4972369c04e8.docx"
## [551] "INTRODUCTION TO AFRICA -- LECTURE NOTES - 2.docx"
## [552] "INTRODUCTION TO AFRICA.docx"
## [553] "Invasive Species-Carson-Final-2 (1).ppt"
## [554] "Invasive Species-Carson-Final-2 (2).ppt"
## [555] "Invasive Species-Carson-Final-2 (3).ppt"
## [556] "Invasive Species-Carson-Final-2.ppt"
## [557] "IWA PART 1 MIDTERM ESSAY (1).docx"
## [558] "IWA PART 1 MIDTERM ESSAY (2).docx"
## [559] "IWA PART 1 MIDTERM ESSAY.docx"
## [560] "IWA PART 2 ART in Quarantine (1).docx"
## [561] "IWA PART 2 ART in Quarantine.docx"
## [562] "Jade.Axe"
## [563] "JC #1 - Hegazy, Kabiel, and Fawzy (2009) (1).pptx"
## [564] "JC #1 - Hegazy, Kabiel, and Fawzy (2009).pptx"
## [565] "JC #2 - Paolacci, Jansen, and Harrison (2018).pptx"
## [566] "Jeffrey H. Reiman_ Paul Leighton - The Rich Get Richer and the Poor Get Prison_ Ideology, Class, and Criminal Justice (2016, Routledge) - libgen.lc 2.pdf"
## [567] "John Creasy_HandMade with Soil (1).pdf"
## [568] "John Creasy_HandMade with Soil.pdf"
## [569] "John Esposito Chemistry 0120 Recitation and Office Hours Links (1).pdf"
## [570] "John Esposito Chemistry 0120 Recitation and Office Hours Links.pdf"
## [571] "Jounral Bio 1 thing (1).pdf"
## [572] "Jounral Bio 1 thing (2).pdf"
## [573] "Jounral Bio 1 thing.pdf"
## [574] "Jounral CLub #2.pdf"
## [575] "Jounral CLub #2.pptx"
## [576] "JUNIOR DRIVER'S LICENSE.pdf"
## [577] "Key to practice questions.pdf"
## [578] "KeyExam3MW.doc"
## [579] "Khafre.Qin.APAP.reading.pdf"
## [580] "KindleForMac-1.30.59055.dmg"
## [581] "Krishna Final Revision.pdf"
## [582] "Krishna Paper 1 (1).pdf"
## [583] "Krishna Paper 1 (2).pdf"
## [584] "Krishna Paper 1.pdf"
## [585] "Krishna Paper Three (1).pdf"
## [586] "Krishna Paper Three (2).pdf"
## [587] "Krishna Paper Three (3).pdf"
## [588] "Krishna Paper Three.pdf"
## [589] "Krishna Paper Two (1).pdf"
## [590] "Krishna Paper Two (2).pdf"
## [591] "Krishna Paper Two (3).pdf"
## [592] "Krishna Paper Two Revision.pdf"
## [593] "Krishna Paper Two.pdf"
## [594] "KrishnaPatel_Electronic Fine Slip.pdf"
## [595] "Kurten&Carson_2015_BioSci(4) copy (1).pdf"
## [596] "Kurten&Carson_2015_BioSci(4) copy.pdf"
## [597] "L1.3 Biomolecules Overview Slides and Study Guide.pdf"
## [598] "Lab 01 Report - Changing Motion.docx"
## [599] "Lab 03 Report - Combining Forces.docx"
## [600] "Lab 05 Report - Two Dimensional Motion (Projectile Motion) (1).docx"
## [601] "Lab 05 Report - Two Dimensional Motion (Projectile Motion).docx"
## [602] "Lab 06 Report - Conservation of Energy.docx"
## [603] "Lab 07 Report - Voltage in Simple DC Circuits and Ohms Law.docx"
## [604] "Lab 1 (1).pdf"
## [605] "Lab 1 .pdf"
## [606] "Lab 10 .pdf"
## [607] "Lab 10 Prelab.pdf"
## [608] "lab 11.pdf"
## [609] "Lab 4 (1).pdf"
## [610] "Lab 4 gen cehm 1 (1).pdf"
## [611] "Lab 4 gen cehm 1.pdf"
## [612] "Lab 4.pdf"
## [613] "Lab 5 pt.2.pdf"
## [614] "Lab 5 .pdf"
## [615] "lab 5'.pdf"
## [616] "Lab 6 pl.pdf"
## [617] "Lab 6.pdf"
## [618] "Lab 8 .pdf"
## [619] "Lab 8 Prelan .pdf"
## [620] "Lab 8 try 2.pdf"
## [621] "Lab 9 pre lab .pdf"
## [622] "lab 9.pdf"
## [623] "Lab Meeting 2 Daphnia Excel sheet 3.25.21 (1).xlsx"
## [624] "Lab Meeting 2 Daphnia Excel sheet 3.25.21.xlsx"
## [625] "Lab Meeting_Community Experiment.docx"
## [626] "labsyllabus_0120_2214.pdf"
## [627] "least_squares_intro-2.pdf"
## [628] "Lecture 1.2- Water and Bonding Powerpoint and Study Guide.pdf"
## [629] "Lecture 1.4- Carbohydrates Powerpoint and Study Guide.pdf"
## [630] "Lecture 1.5- Lipids Powerpoint and Study Guide.pdf"
## [631] "Lecture 1.7- RNA Structure and Function Powerpoint and Study Guide.pdf"
## [632] "Lecture 1.9- Translation Powerpoint and Study Guide.pdf"
## [633] "Lecture 7 Practice Problem (Solutions)_20200905_0001.pdf"
## [634] "Lecture B Beyond Mendel Fall 2022 no signaling epistasis no pedigree.pptx"
## [635] "Lecture B Beyond Mendel Fall 2022 pre no signaling epistasis no pedigree.pdf"
## [636] "Lecture C Chromosome theory 2022 for Quiz 1.pptx"
## [637] "Lecture F Mutations Fall 2022.pptx"
## [638] "Lecture G1 Genetic code 2022 2.pptx"
## [639] "Lecture G1 Genetic code 2022 pre.pdf"
## [640] "Lecture G2 Trancription 2022 pre.pdf"
## [641] "Lecture G3 Translation 2022 pre.pdf"
## [642] "Lecture G4 Mutations 2 2022 pre (1).pdf"
## [643] "Lecture G4 Mutations 2 2022 pre (2).pdf"
## [644] "Lecture G4 Mutations 2 2022 pre (3).pdf"
## [645] "Lecture G4 Mutations 2 2022 pre.pdf"
## [646] "Lecture G4 Mutations 2 2022.pptx"
## [647] "Lecture H Molecular Genetic Techniques 2022 pre (1).pdf"
## [648] "Lecture H Molecular Genetic Techniques 2022 pre (2).pdf"
## [649] "Lecture H Molecular Genetic Techniques 2022 pre (3).pdf"
## [650] "Lecture H Molecular Genetic Techniques 2022 pre (4).pdf"
## [651] "Lecture H Molecular Genetic Techniques 2022 pre.pdf"
## [652] "Lecture I Molecular Analysis of Genomes 2022 (1).pptx"
## [653] "Lecture I Molecular Analysis of Genomes 2022 pre.pdf"
## [654] "Lecture I Molecular Analysis of Genomes 2022.pptx"
## [655] "Lecture J Chromosomes 2022 2.pptx"
## [656] "Lecture J Chromosomes 2022 pre.pdf"
## [657] "Lecture K Chromosome abnormalities 2022 pre.pdf"
## [658] "Lecture K Chromosome abnormalities 2022.pptx"
## [659] "Lecture L Bacterial genetics 2022 pre.pdf"
## [660] "Lecture L,M,N Bacterial genetics 2022.pptx"
## [661] "Lecture Predation and Herbivory Part II-1-9 (1).ppt"
## [662] "Lecture Predation and Herbivory Part II-1-9.ppt"
## [663] "lecture-introd2RStudio-with_scripts.pdf"
## [664] "Lecture02 (1).pdf"
## [665] "Lecture02 (2).pdf"
## [666] "Lecture02.pdf"
## [667] "Lecture04.pdf"
## [668] "Lecture05.pdf"
## [669] "Lecture06 (1).pdf"
## [670] "Lecture06.pdf"
## [671] "Lecture08.pdf"
## [672] "Letter of Interst Dr. Kontos.docx"
## [673] "Letter to Class of 2025 - Google Docs.pdf"
## [674] "Lib assignment .pdf"
## [675] "Libraynth (1).pdf"
## [676] "Libraynth (2).pdf"
## [677] "Libraynth (3).pdf"
## [678] "Libraynth .pdf"
## [679] "line_of_best_fit_example-tibet_allele_freq (1).pdf"
## [680] "line_of_best_fit_example-tibet_allele_freq.pdf"
## [681] "Love on the Sahel essay .pdf"
## [682] "M Gene reg bacteria 2022 pre.pdf"
## [683] "M Gene reg bacteria Fall 2021 pre.pdf"
## [684] "M Gene reg bacteria Fall 2022.pptx"
## [685] "M3.Khafre.Qin (1).pdf"
## [686] "M3.Khafre.Qin.pdf"
## [687] "Mapping the Global Muslim Population.pdf"
## [688] "meeting-91999866091.ics"
## [689] "meeting-93219672601 (1).ics"
## [690] "meeting-93219672601 (2).ics"
## [691] "meeting-93219672601 (3).ics"
## [692] "meeting-93219672601.ics"
## [693] "Meiners and Pickett 2011(3).pdf"
## [694] "Melies Brewer pp 370-371 (1).pdf"
## [695] "Melies Brewer pp 370-371 (2).pdf"
## [696] "Melies Brewer pp 370-371.pdf"
## [697] "Micro_NEW Major_Tracker 2.pdf"
## [698] "Micro_NEW Major_Tracker.pdf"
## [699] "Microsoft Word - Sharpley Tourism Notes iMac.docx"
## [700] "Microsoft Word - Sharpley Tourism Notes iMac.docx.pdf"
## [701] "Mid term Art 1 (1).docx"
## [702] "Mid term Art 1.docx"
## [703] "Mid term Pics (1).docx"
## [704] "Mid term Pics (2).docx"
## [705] "Mid term Pics.docx"
## [706] "midterm exam review - Anneliese.pdf"
## [707] "Midterm Review Material (1).pdf"
## [708] "Midterm Review Material (2).pdf"
## [709] "Midterm Review Material (3).pdf"
## [710] "Midterm Review Material Key (1).pdf"
## [711] "Midterm Review Material Key.pdf"
## [712] "Midterm Review Material.pdf"
## [713] "Midterm review sheet fall 2022.docx"
## [714] "MIles and Henry_Gender.pdf"
## [715] "Muslim_Astronomers_who_Influenced_Copern.pdf"
## [716] "Mutualism Lecture-Final-2-1-2 (1).pptx"
## [717] "Mutualism Lecture-Final-2-1-2.pptx"
## [718] "my_SNP"
## [719] "N Gene reg eukaryotes 2022 for quiz 6.pptx"
## [720] "N Gene reg eukaryotes 2022 pre.pdf"
## [721] "N Gene reg eukaryotes Fall 2021 for Quiz 7.pptx"
## [722] "Nancy Pearcey-1 (1).pdf"
## [723] "Nancy Pearcey-1.pdf"
## [724] "Nasser Abufarha_ Neil L. Whitehead_ Jo Ellen Fair_ Leigh A.Payne - The Making of a Human Bomb_ An Ethnography of Palestinian Resistance-Duke University Press Books (2009).pdf"
## [725] "NMR1-3_ChemicalShift_V2-Slides (1).pdf"
## [726] "NMR1-3_ChemicalShift_V2-Slides.pdf"
## [727] "NMR2-2_Solvents_V2-Slides (1).pdf"
## [728] "NMR2-2_Solvents_V2-Slides.pdf"
## [729] "NMR2-3_ComplexSplitting_V2-Slides.pdf"
## [730] "NMR2-4_LongRangeCoupling_V2-Slides.pdf"
## [731] "Note card 2 - Google Docs.pdf"
## [732] "Note card 2 pt2 (1).pdf"
## [733] "Note card 2 pt2 (2).pdf"
## [734] "Note card 2 pt2.odt"
## [735] "Note card 2 pt2.pdf"
## [736] "Note Feb 10, 2022 2.pdf"
## [737] "Note Feb 10, 2022 3.pdf"
## [738] "Note Feb 10, 2022 4.pdf"
## [739] "Note Feb 10, 2022.pdf"
## [740] "Note Feb 17, 2022.pdf"
## [741] "Note Feb 24, 2022.pdf"
## [742] "Nuttle et al. 2013 (1).pdf"
## [743] "Nuttle et al. 2013 (2).pdf"
## [744] "Nuttle et al. 2013 (3).pdf"
## [745] "Nuttle et al. 2013.pdf"
## [746] "O Manipulating eukaryotic genomes 2022 pre.pdf"
## [747] "O Manipulating eukaryotic genomes 2022.pptx"
## [748] "Organic Chemistry Structure and Function by K. Peter C. Vollhardt (z-lib.org).pdf"
## [749] "Packet1PERadiologyMonitoringFo.pdf"
## [750] "paley essay (1).pdf"
## [751] "paley essay (2).pdf"
## [752] "paley essay.pdf"
## [753] "Pasztory_ Thinking Things.pdf"
## [754] "Patel_Dark_Crystal.mp4"
## [755] "PCA-missing_data.Rmd"
## [756] "periodic-table.pdf"
## [757] "PeriodicTableMuted-56a12d823df78cf772682aaa.png"
## [758] "Permaculture handout (1).pdf"
## [759] "Permaculture handout (2).pdf"
## [760] "Permaculture handout.pdf"
## [761] "phage (1).fasta"
## [762] "phage (2).fasta"
## [763] "phage.fasta"
## [764] "Pham16216Report.pdf"
## [765] "Pham49320Report.pdf"
## [766] "Philo ON CREATION.pdf"
## [767] "PHYS 0111 Chapter 13 Fall 2022 (1).pdf"
## [768] "PHYS 0111 Chapter 13 Fall 2022.pdf"
## [769] "PHYS 0111 Chapter 14 Fall 2022 (1).pdf"
## [770] "PHYS 0111 Chapter 14 Fall 2022.pdf"
## [771] "PHYS 0111 Chapter 15 Fall 2022 (1).pdf"
## [772] "PHYS 0111 Chapter 15 Fall 2022.pdf"
## [773] "PHYS 0111 Chapter 22 Fall 2022.pdf"
## [774] "PHYS 0111 Chapter 23 Fall 2022.pdf"
## [775] "PHYS 0111 Chapter 24 Fall 2022 (1).pdf"
## [776] "PHYS 0111 Chapter 24 Fall 2022.pdf"
## [777] "PHYS 0111 Chapter 25 Fall 2022.pdf"
## [778] "PHYS 0111 Chapter 27 Fall 2022.pdf"
## [779] "PHYS 0111 Equation Sheet Fall 2022 (1).pdf"
## [780] "PHYS 0111 Equation Sheet Fall 2022 (2).pdf"
## [781] "PHYS 0111 Equation Sheet Fall 2022 (3).pdf"
## [782] "PHYS 0111 Equation Sheet Fall 2022 (4).pdf"
## [783] "PHYS 0111 Equation Sheet Fall 2022 (5).pdf"
## [784] "PHYS 0111 Equation Sheet Fall 2022.pdf"
## [785] "PHYS2201-notes-ch2.pdf"
## [786] "Picture1.png"
## [787] "Pitt Ecology-Nov-2021.pptx"
## [788] "Plagiarism – The Writing Center • University of North Carolina at Chapel Hill.pdf"
## [789] "Plant Love and Plant Detectives.pptx"
## [790] "Plue et al. 2019.13201-1.pdf"
## [791] "pollutant websearch.docx"
## [792] "pond_site_analysis_template_to_fill_sp21 (1).pptx"
## [793] "pond_site_analysis_template_to_fill_sp21.pptx"
## [794] "Population Genetics Invasion Lecture Nov. 15 (1).pdf"
## [795] "Population Genetics Invasion Lecture Nov. 15.pdf"
## [796] "Portfolio Working direct"
## [797] "portfolio_ggpubr_intro-2 (1).Rmd"
## [798] "portfolio_ggpubr_intro-2 (2).Rmd"
## [799] "portfolio_ggpubr_intro-2 (3).Rmd"
## [800] "portfolio_ggpubr_intro-2 (4) (Autosaved).rmd"
## [801] "portfolio_ggpubr_intro-2 (4).Rmd"
## [802] "portfolio_ggpubr_intro-2 (5).Rmd"
## [803] "portfolio_ggpubr_intro-2 (6).Rmd"
## [804] "portfolio_ggpubr_intro-2.Rmd"
## [805] "portfolio_ggpubr_log_transformation.Rmd"
## [806] "portfolio-01-dataframe.ipynb"
## [807] "Position (m) copy.jpg"
## [808] "Post lab 3.pdf"
## [809] "Post lab 4.pdf"
## [810] "Post lab 5.pdf"
## [811] "Post lab 6.pdf"
## [812] "Post lab 7,8.pdf"
## [813] "Post lab 9.pdf"
## [814] "Pre lab 7 .pdf"
## [815] "PRE-COLONIAL AFRICAN HISTORY AND MISCONCEPTION OF AFRICA (1).pdf"
## [816] "PRE-COLONIAL AFRICAN HISTORY AND MISCONCEPTION OF AFRICA (2).pdf"
## [817] "PRE-COLONIAL AFRICAN HISTORY AND MISCONCEPTION OF AFRICA (3).pdf"
## [818] "PRE-COLONIAL AFRICAN HISTORY AND MISCONCEPTION OF AFRICA.pdf"
## [819] "Prelab Activity 3 .pdf"
## [820] "Prelab for lab 4.pdf"
## [821] "Presentation planning DWS sp21_post.docx"
## [822] "Presentation1.pptx"
## [823] "Preziosi&Farago_ Art is Not What You Think It Is (1).pdf"
## [824] "Preziosi&Farago_ Art is Not What You Think It Is.pdf"
## [825] "Princess Bride pt.2 (1).docx"
## [826] "Princess Bride pt.2 (2).docx"
## [827] "Princess Bride pt.2 (2).ps"
## [828] "Princess Bride pt.2 (3).docx"
## [829] "Princess Bride pt.2.docx"
## [830] "Princess Bride pt.2.pdf"
## [831] "Problems 5 Spring 2022 updated.pdf"
## [832] "Propp Morphology pp 24-59 (1).pdf"
## [833] "Propp Morphology pp 24-59.pdf"
## [834] "ProtonVPN.dmg"
## [835] "psf_forest_community_dynamics.pptx"
## [836] "Q Genetics of Cancer 2022.pptx"
## [837] "Quiz+1 (2).pdf"
## [838] "Quiz+1.pdf"
## [839] "Quiz+2 (2).pdf"
## [840] "Quiz+2.pdf"
## [841] "Quiz+3 (1).pdf"
## [842] "Quiz+3 (2).pdf"
## [843] "Quiz+3.pdf"
## [844] "Quiz+4 (2).pdf"
## [845] "Quiz+6.pdf"
## [846] "Quiz+7.pdf"
## [847] "Quiz+8.pdf"
## [848] "quizlog1.pdf"
## [849] "R_data_structures_vectors_intro.pdf"
## [850] "R4.3.pptx"
## [851] "reading list 9-2019"
## [852] "reading list 9-2019.zip"
## [853] "Reading List Add ons 2021"
## [854] "Reading List Add ons 2021.zip"
## [855] "Recitation 1 2021 Spring 2022.docx"
## [856] "Recitation 1.3 Q1 Table.png"
## [857] "Recitation 13 (1).pptx"
## [858] "Recitation 13 (2).pptx"
## [859] "Recitation 13.pptx"
## [860] "Recitation 6 2022.docx"
## [861] "Recitation 7 Spring 2022.docx"
## [862] "Recitation 8 Spring 2022.docx"
## [863] "Recitation 9.pptx"
## [864] "Recitation week 4.pdf"
## [865] "Recitation_Week_12_copy.pdf"
## [866] "Recitation12.pptx"
## [867] "Recitiation 29th.pdf"
## [868] "Reflection #2 (1).pdf"
## [869] "Reflection #2 (2).pdf"
## [870] "Reflection #2 (3).pdf"
## [871] "Reflection #2.pdf"
## [872] "Reflections Religion and Science (1).pdf"
## [873] "Reflections Religion and Science (2).pdf"
## [874] "Reflections Religion and Science (3).pdf"
## [875] "Reflections Religion and Science (4).pdf"
## [876] "Reflections Religion and Science (5).pdf"
## [877] "Reflections Religion and Science (6).pdf"
## [878] "Reflections Religion and Science (7).pdf"
## [879] "Reflections Religion and Science.pdf"
## [880] "Reiman CH 2(1) (2).docx"
## [881] "Reiman CH 3(2) (1).docx"
## [882] "Reiman chapter 1.docx"
## [883] "Reiman Intro (2) (1).docx"
## [884] "Reiman Intro (2).docx"
## [885] "Relfection #3 (1).docx"
## [886] "Relfection #3.docx"
## [887] "Religon and science final .docx"
## [888] "Reliogn and science paper.docx"
## [889] "removing_fixed_alleles.Rmd"
## [890] "ResponseSummary.pdf"
## [891] "Resume 2.docx"
## [892] "Resume.docx"
## [893] "Review Questions Exam 3-1.pdf"
## [894] "Review Questions Exam 4.pdf"
## [895] "Rewilding Discussion Questions-4.docx"
## [896] "Ripple&Beschta_2012_BioCons-1.pdf"
## [897] "Robert J. Debry Essay.pdf"
## [898] "Ronald L. Numbers - Galileo Goes to Jail and Other Myths about Science and Religion-Harvard University Press (2009).pdf"
## [899] "rsconnect"
## [900] "RStudio-2022.07.1-554.dmg"
## [901] "RStudio-2022.07.2-576 (1).dmg"
## [902] "RStudio-2022.07.2-576.dmg"
## [903] "salt in duckweed (1) (1).pptx"
## [904] "salt in duckweed (1).pptx"
## [905] "salt in duckweed.pptx"
## [906] "sampling distribution for mean.png"
## [907] "Savage.K.Monument.Wars.on.Lin (1).pdf"
## [908] "Savage.K.Monument.Wars.on.Lin.pdf"
## [909] "Savanna Hoemcoming .pdf"
## [910] "schedule.ics"
## [911] "Schedule.pdf"
## [912] "Schnitzer and Carson 2010 (1).pdf"
## [913] "Schnitzer and Carson 2010.pdf"
## [914] "Schnitzer and Carson Study Questions-1 (1).docx"
## [915] "Schnitzer and Carson Study Questions-1.docx"
## [916] "Scholarly Literature Search_Duckweed Sp21_3.7.2021.docx"
## [917] "SCIENCE AND RELIGION Syllabus Spring 2021-1.pdf"
## [918] "Science communication .docx"
## [919] "SCIGRESS_V3.3.3.dmg"
## [920] "SCIGRESS_V3.4.3 (1).dmg"
## [921] "SCIGRESS_V3.4.3.dmg"
## [922] "Screen Shot 2020-08-25 at 9.57.06 PM.png"
## [923] "Screen Shot 2022-09-04 at 6.40.11 PM.png"
## [924] "Screen Shot 2022-10-06 at 8.12.34 PM.png"
## [925] "Screen Shot 2022-10-11 at 9.58.45 PM copy (1).jpg"
## [926] "Screen Shot 2022-10-11 at 9.58.45 PM copy.jpg"
## [927] "Screen Shot 2022-10-17 at 3.16.22 PM (1).png"
## [928] "Screen Shot 2022-10-17 at 3.16.22 PM.png"
## [929] "Screen Shot 2022-10-19 at 3.37.01 PM (1).png"
## [930] "Screen Shot 2022-10-19 at 3.37.01 PM.png"
## [931] "Screen Shot 2022-10-31 at 3.25.36 PM.png"
## [932] "Screen Shot 2022-12-01 at 4.37.11 PM.jpg"
## [933] "Screen_Shot_2021-01-27_at_1.04.23_PM.png"
## [934] "Screen_Shot_2021-02-03_at_1.34.47_PM.png"
## [935] "Screen_Shot_2021-02-03_at_12.47.59_PM (1).png"
## [936] "Screen_Shot_2021-02-03_at_12.47.59_PM.png"
## [937] "Screen_Shot_2021-02-03_at_12.49.40_PM.png"
## [938] "Screen_Shot_2021-02-10_at_2.55.15_PM.png"
## [939] "Screen_Shot_2021-02-10_at_3.01.41_PM.png"
## [940] "Screen_Shot_2021-04-14_at_1.00.15_PM.png"
## [941] "Sharpley Tourism Notes iMac.pdf"
## [942] "ShoulderBraceStudy.pdf"
## [943] "Simmons - Odd Girl Out (1).pdf"
## [944] "Simmons - Odd Girl Out.pdf"
## [945] "Slavery and emancipation lecture Handout.pdf"
## [946] "Slavery and emancipation lecture PP.pptx"
## [947] "SOC 0005 Globalization Notes 2020.docx"
## [948] "SOC 0005- A Growing Trend of Leaving America.doc"
## [949] "Soc of Tourism - Approaches, Issues & Findings (Cohen).pdf"
## [950] "Societies 2211 (1).docx"
## [951] "Societies 2211.docx"
## [952] "Sociology of Tourism Cohen .docx"
## [953] "Sociology of Tourism Notes (3).docx"
## [954] "Sociology of Tourism Notes II (1).docx"
## [955] "Socities Exam 3notes.docx"
## [956] "Socitites CH4 Remian.doc"
## [957] "SolsticeClientMac_V2A0AE303CDPCF6CI8ECC0BD6.app"
## [958] "SolsticeClientMac_V2A0AE303CDPCF6CI8ECC0BD6.zip"
## [959] "Solution to Chapter 2 End Problems.pdf"
## [960] "Special Notes on Welfare(1).docx"
## [961] "SpotifyInstaller (1).zip"
## [962] "SpotifyInstaller.zip"
## [963] "Spring 2021 Tution poayment .pdf"
## [964] "SR Online Extra Credit Opportunities.docx"
## [965] "ST_1000__Practice_Midterm_2_S22.pdf"
## [966] "STAT_1000___HW_2_S_22.pdf"
## [967] "STAT_1000___S22___1085.pdf"
## [968] "STAT_1000__Extra_Credit_S22.pdf"
## [969] "STAT_1000__HW_1_S22.pdf"
## [970] "STAT_1000__HW_4_S22.pdf"
## [971] "STAT_1000__HW_5_S22%281%29.pdf"
## [972] "STAT_1000__HW_6_S22.pdf"
## [973] "STAT_1000__HW_7_S22.pdf"
## [974] "STAT_1000__HW_8_S22.pdf"
## [975] "STAT_1000__More_on_Hypothesis_Testing_SP___Slides.pdf"
## [976] "STAT_1000__Practice_Problem__Solutions_.pdf"
## [977] "STAT_1000__Practice_Problems__Final__F21.pdf"
## [978] "STAT_1000__Quiz_10.pdf"
## [979] "STAT_1000__Quiz_11_S22.pdf"
## [980] "STAT_1000__Quiz_12_S22.pdf"
## [981] "STAT_1000__Quiz_9.pdf"
## [982] "STAT_1000_HW_3_S_22.pdf"
## [983] "Stats quiz 5.pdf"
## [984] "steam.dmg"
## [985] "Study Guide to Private Life of Plants - Social Struggle.pdf"
## [986] "Study questions for Carson et al 2008.docx"
## [987] "Study Questions for Hirsch et al. 2014FINAL-2.docx"
## [988] "submission_99715463.pdf"
## [989] "summary_stats.pdf"
## [990] "Survivorship in the Natural World - Honors College Homework 3.docx"
## [991] "Sutton et al. 2021 (1).pdf"
## [992] "Sutton et al. 2021 (2).pdf"
## [993] "Sutton et al. 2021.pdf"
## [994] "Syllabus PHYS 0111 10429 Fall 2022.pdf"
## [995] "Teamwork semester evaluation.docx"
## [996] "Technology Preparation_Duckweed Survivor_klw1.13.21.docx"
## [997] "TEME.pdf"
## [998] "Templete.pdf"
## [999] "The princess bride essay (1).pdf"
## [1000] "The princess bride essay final draft.pdf"
## [1001] "The princess bride essay.pdf"
## [1002] "Timaeus-1 (1).pdf"
## [1003] "Timaeus-1 (2).pdf"
## [1004] "Timaeus-1.pdf"
## [1005] "Time series plots from vectors (1).pdf"
## [1006] "Tropical Ecology - Top down effects-Panama-.pptx"
## [1007] "Unconfirmed 145395.crdownload"
## [1008] "Unconfirmed 174225.crdownload"
## [1009] "Unconfirmed 283790.crdownload"
## [1010] "Unconfirmed 398081.crdownload"
## [1011] "Unconfirmed 446809.crdownload"
## [1012] "Untitled document (1).pdf"
## [1013] "Untitled document (2).pdf"
## [1014] "Untitled document.pdf"
## [1015] "Untitled.docx"
## [1016] "Untitled.Rmd"
## [1017] "Vander Ven CH 1.doc"
## [1018] "Vander Ven CH 2 -3.doc"
## [1019] "Vander Ven CH 4.doc"
## [1020] "Vander Ven CH 5.doc"
## [1021] "Vander Ven CH 6.doc"
## [1022] "Vander Ven Lecture Notes Final (5).docx"
## [1023] "vcfR_test.vcf"
## [1024] "vcfR_test.vcf.gz"
## [1025] "vegan_PCA_amino_acids-STUDENT_files"
## [1026] "vegan_PCA_amino_acids-STUDENT.Rmd"
## [1027] "VidyoConnect"
## [1028] "VidyoConnectInstaller-macosx-TAG_VCOND_20_2_0_13382[p=https&h=epiccal.video.upmc.com&x=1&f=RzpJUENPOklQQ0k6TW9kOlBDOlB1YkM6Q0RSOkVQOkNQOlJQSTpCQTpOREM6Q1BSOk9BOjIyMDpQUjpTUjI6U1I=&r=BLHNysomvy].dmg"
## [1029] "VRRENEWAL.pdf"
## [1030] "Wednesday Community Master File_day14_sp21.xlsx"
## [1031] "Wee 6 academic foundations (1).pdf"
## [1032] "Wee 6 academic foundations.pdf"
## [1033] "Week 11 - Recitation (1).pdf"
## [1034] "Week 11 - Recitation.pdf"
## [1035] "Week 11 Recitation Background.pdf"
## [1036] "Week 12 (Nov 15) class slides-1 (1).pptx"
## [1037] "Week 12 (Nov 15) class slides-1.pptx"
## [1038] "Week 12 (Nov 15) full slides-1.pptx"
## [1039] "Week 12 Recitation (1).pdf"
## [1040] "Week 12 Recitation.pdf"
## [1041] "Week 14 (Nov 29) full slides.pptx"
## [1042] "Week 3 Recitation.pdf"
## [1043] "Week 3 Sept 13 class slides.pptx"
## [1044] "Week 4 Recitation.pdf"
## [1045] "Week 4 Sept 20 BLAST class slides.pptx"
## [1046] "Week 4 Sept 20 BLAST full slides.pptx"
## [1047] "Week 5 Sept 27 class slides.pptx"
## [1048] "Week 5 Study Guide & PPT Slides (1).pdf"
## [1049] "Week 5 Study Guide & PPT Slides.pdf"
## [1050] "Week 6 Oct 4 class slides.pptx"
## [1051] "Week 6 Oct 4 full slides.pptx"
## [1052] "Week 6 Study Guide SV2 (1).pdf"
## [1053] "Week 6 Study Guide SV2 (2).pdf"
## [1054] "Week 6 Study Guide SV2.pdf"
## [1055] "Week 7 Recitation.pdf"
## [1056] "Week 7 Study Guide SV.pdf"
## [1057] "Week 8 Oct 18 full slides (1).pptx"
## [1058] "Week 8 Oct 18 full slides (2).pptx"
## [1059] "Week 8 Oct 18 full slides.pptx"
## [1060] "Week 8 Population Experiment Part 2 - Guidance.pptx"
## [1061] "Week 9 (Oct 25) full slides (1).pptx"
## [1062] "Week 9 (Oct 25) full slides.pptx"
## [1063] "Welcome to FALL Semester 2211 (1).docx"
## [1064] "Welcome to FALL Semester 2211 (2).docx"
## [1065] "Welcome to FALL Semester 2211 (3).docx"
## [1066] "Welcome to FALL Semester 2211.docx"
## [1067] "What is computational biology_ (1) (1).pdf"
## [1068] "What is computational biology_ (1).pdf"
## [1069] "Why Difficult Movies Are More, Um, Difficult - The New York Times (1).pdf"
## [1070] "Why Difficult Movies Are More, Um, Difficult - The New York Times (2).pdf"
## [1071] "Why Difficult Movies Are More, Um, Difficult - The New York Times.pdf"
## [1072] "working version.xlsx"
## [1073] "Yancey Martin and Hummer - Fraternities and Rape on Campus.pdf"
## [1074] "your-ap-score-report-unofficial-copy.pdf"
## [1075] "Zallek Ecology Guest Lecture 11.16.21 (1) (1).pdf"
## [1076] "Zallek Ecology Guest Lecture 11.16.21 (1).pdf"
## [1077] "Zoom.pkg"
## [1078] "ztable.pdf" #TODO
list.files(pattern = "vcf") ## [1] "1189983.vcf"
## [2] "all_loci-1.vcf"
## [3] "all_loci.vcf"
## [4] "ALL.chr10_GRCh38.genotypes.20170504.vcf.gz"
## [5] "code_checkpoint_vcfR.html"
## [6] "code_checkpoint_vcfR.Rmd"
## [7] "vcfR_test.vcf"
## [8] "vcfR_test.vcf.gz" #TODO
warning("Friendly remindeR: Make sure you have set your working directory")## Warning: Friendly remindeR: Make sure you have set your working directoryFourth, load the .vcf file.
# call vcfR::read.vcfR()
bird_snps_again <- vcfR::read.vcfR("all_loci.vcf",
convertNA = T) #TODO## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 1929
## column count: 81
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 1929
## Character matrix gt cols: 81
## skip: 0
## nrows: 1929
## row_num: 0
##
Processed variant 1000
Processed variant: 1929
## All variants processedwarning("RemindeR: If this didn't work, you may not have set your working directory to the location of the vcf file")## Warning: RemindeR: If this didn't work, you may not have set your working
## directory to the location of the vcf fileFifth, convert to numeric genotypic score (counts of the number of
the minor allele) with vcfR::extract.gt().
# call vcfR::extract.gt()
bird_snps_num_again <- vcfR::extract.gt(bird_snps_again, # TODO
element = "GT",
IDtoRowNames = F,
as.numeric = T,
convertNA = T)Sixth, transpose the data into the format that works with R with
t().
# call t() on bird_snps_num_again
bird_snps_num_t_again <- t(bird_snps_num_again) # TODOSeventh, remove the invariant columns with
invar_omit().
# call invar_omit() on bird_snps_num_t_again
bird_snps_no_invar <- invar_omit(bird_snps_num_t_again) #TODO## Dataframe of dim 72 1929 processed...
## 590 columns removedCompare the original and the new dfs
# call dim() on bird_snps_num_t_again
dim(bird_snps_num_t_again) #TODO## [1] 72 1929# call dim() on bird_snps_no_invar
dim(bird_snps_no_invar) #TODO## [1] 72 1339These data have a lot of NAs. If we just call na.omit()
on them, what happens? Call na.omit() on the
bird_snps_num_t_again object, then check the
dimensions.
# Call na.omit() on bird_snps_num_t
## and assign the output to no_NAs
no_NAs <- na.omit(bird_snps_num_t_again) # TODO
# what is the remaining size of the data?
# why
dim(no_NAs)## [1] 0 1929