NOTE - before you begin, make sure your WORKING DIRECTORY is set to the location of the .vcf file being used.
All of this material will appear on the exam. Take notes on the workflow, functions, and concepts.
getwd() and
list.files(pattern = ...)extract.gt() command doesna.omit() on SNPsWe need just one package for this lesson, vcfR.
library(vcfR)## Warning: package 'vcfR' was built under R version 4.2.2##
## ***** *** vcfR *** *****
## This is vcfR 1.13.0
## browseVignettes('vcfR') # Documentation
## citation('vcfR') # Citation
## ***** ***** ***** *****setwd("C:/Users/jclan/OneDrive - University of Pittsburgh/BIOSC 1540/rStudio/12.3")In this lesson you will be using a .vcf file called
“all_loci.vcf”.
You must make sure that R has its working directory set to where this file is located.
The easiest way to do this is
Check the location of your working directory with
getwd()
# run getwd()
getwd()## [1] "C:/Users/jclan/Downloads" # todoCheck for the presence of the “all_loci.vcf” file in the working
directory with list.files()
# run list.files()
list.files()## [1] "[FEEDBACK]Annotated Outline Team 34 Langella Laug Savko.docx"
## [2] "0110 F20 Recitation Worksheet 2 Send (1).pdf"
## [3] "0110 F20 Recitation Worksheet 2 Send.pdf"
## [4] "0110 F20 420 PM Syllabus Convert Upload (1).pdf"
## [5] "0110 F20 420 PM Syllabus Convert Upload.pdf"
## [6] "0110 F20 420 PM Syllabus Updated with Canvas Compliance (1).pdf"
## [7] "0110 F20 420 PM Syllabus Updated with Canvas Compliance (2).pdf"
## [8] "0110 F20 420 PM Syllabus Updated with Canvas Compliance.pdf"
## [9] "0110 F20 Chapter 4 Openstax Text End of Chapter Questions Post Updated.docx"
## [10] "0110 F20 Chapter 5 Thermochemistry Notes for Students.pdf"
## [11] "0110 F20 Recitation Worksheet 1 For Students.pdf"
## [12] "0110 F20 Rules for Drawing Lewis Structures Post on Canvas.pdf"
## [13] "0110 F20 Schedule Updated Post.pdf"
## [14] "0110 F20 Schedule Updated With Final Exam Day and Time.pdf"
## [15] "0110 FP20 OpenStax Chapter 4 Notes for Students to Use.pdf"
## [16] "0120 SP21 Openstax Chapter 14 Acid-Base Equilibria.pdf"
## [17] "0120 SP21 Openstax Chapter 14 Acid Base Equilibria for Students 325 March 10.pdf"
## [18] "0120 SP21 Recitation Worksheet 1 Chapter 10 for Students.pdf"
## [19] "0240_sample_final_1.pdf"
## [20] "10.34543678-34783678.ALL.chr10_GRCh38.genotypes.20170504.vcf.gz"
## [21] "12_3_DoubleIntegralsPolar.pdf"
## [22] "12_7_SphericalCoordinates.pdf"
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## [24] "1434255.pdf"
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## [26] "1930_2001.txt"
## [27] "2017Exam1Q.pdf"
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## [29] "2018Exam1Q.pdf"
## [30] "2018Exam1Qsol.pdf"
## [31] "2018Exam2Q.pdf"
## [32] "2020-08-26IntroExcel.xlsx"
## [33] "2020-2021_College_Democrats_Constitution_(4).pdf"
## [34] "2020-Democratic-Party-Platform.pdf"
## [35] "2021_09_04_derpy-perry-18840222.png"
## [36] "2022 ARC 0116 - building (model).pdf"
## [37] "2022 ARC 0116 - building (template).ppt"
## [38] "2022 ARC 0116 - week 3 assignment 1 (handout) (1).pdf"
## [39] "2022 ARC 0116 - week 3 assignment 1 (handout).pdf"
## [40] "2022 ARC 0116 - week 3.1 reproduction.pdf"
## [41] "2231 - 0320 - Problem Set 1 (Blank) (1).pdf"
## [42] "2231 - 0320 - Problem Set 1 (Blank).pdf"
## [43] "2231 - 0320 - Problem Set 12 (Blank).pdf"
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## [51] "2231 - 0320 - Problem Set 2 (Blank).pdf"
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## [62] "2231 - 0320 - Problem Set 3 (Blank).pdf"
## [63] "325947611-Differential-Equations-with-Bou-John-Polking[1116].pdf"
## [64] "3387671187_99bcd82641_o.jpg"
## [65] "4833697.acsm"
## [66] "5-24 Real ID - Johnson.pdf"
## [67] "a1145.pdf"
## [68] "A2.java"
## [69] "a2input.txt"
## [70] "A3.java"
## [71] "AbstammungJonah.jpg"
## [72] "Academic Program Change Form.pdf"
## [73] "acs-periodic-table-poster_download.pdf"
## [74] "acs-periodic-table-poster_web (1).png"
## [75] "acs-periodic-table-poster_web.png"
## [76] "Action.txt"
## [77] "ADE_4.5_Installer.exe"
## [78] "ALL.chr10_GRCh38.genotypes.20170504.vcf.gz"
## [79] "all_loci.vcf"
## [80] "allomtery_3_scatterplot3d (1) (1).Rmd"
## [81] "allomtery_3_scatterplot3d (1).Rmd"
## [82] "Analyzing_Practice_Sequencing_Flowers_F22_JR.pptx"
## [83] "annotated-BIOE%20AND%20ME%20FINAL.docx.pdf"
## [84] "annotated-langella%2Cjonah.assignment1.docx.pdf"
## [85] "Answer Key_Chem 0310_Study guide_FInal exam_Spring 2022.pdf"
## [86] "Answer Key_CHEM0310_Problem Set 8_Spring 2022.pdf"
## [87] "Answer Key_Take Home Exam_Spring 2022 (1).pdf"
## [88] "Answer Key_Take Home Exam_Spring 2022.pdf"
## [89] "appendwrite.java"
## [90] "Arbeitsblatt zu Faust II.docx"
## [91] "armhand.txt"
## [92] "ArrayExample.java"
## [93] "arrayinput-1.txt"
## [94] "arrayinput.txt"
## [95] "Assignment 1 Template (1).docx"
## [96] "Assignment 1 Template (2).docx"
## [97] "Assignment 1 Template.docx"
## [98] "Assignment1.java"
## [99] "aufsatz5.docx"
## [100] "Bacterial_isolation_protocol_Student_version_Flowers_F21.pptx"
## [101] "Benjamin - Work of Art Mechanical Reproduction.pdf"
## [102] "BIOE AND ME FINAL (1).docx"
## [103] "BIOE AND ME FINAL (2).docx"
## [104] "BIOE AND ME FINAL (3).docx"
## [105] "BIOE AND ME FINAL.docx"
## [106] "Book4.xlsx"
## [107] "BPB_spectrophotometry.xlsx"
## [108] "BR-Plant and Plot Slides_Flowers_FA21.docx"
## [109] "BR-Prelab for Bacterial Isolation_Flowers_F21_9.5.21.pptx"
## [110] "BR-Prelab Identifying Isolated Bacteria-1.pptx"
## [111] "BR-Prelab UV Petal Pattern_Flowers_FA21.pptx"
## [112] "BR-Spot plate and UV tolerance Prelab_Flowers_F21-1.pptx"
## [113] "Bridges.csv"
## [114] "Bumke, Die hoef. Dame.pdf"
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## [169] "CA_AvgCommuteTimes.xlsx"
## [170] "Calculus.pdf"
## [171] "case-1030.doc"
## [172] "Case studies connecting teamwork and integrity.pdf"
## [173] "center_function.R"
## [174] "CFU Practice Calculation_Flowers_F21.xlsx"
## [175] "CFU Practice Calculation_Flowers_F22.xlsx"
## [176] "ch6-in-class_examples.zip"
## [177] "Chapter 02 - Programs.zip"
## [178] "Chapter 03- programs.zip"
## [179] "Chapter 04-programs.zip"
## [180] "Chapter 05-programs.zip"
## [181] "Chapter 2_Spring 2022 (1).pdf"
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## [184] "Chapter 2_Spring 2022.pdf"
## [185] "Chapter 3_Spring 2022.pdf"
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## [187] "CHEM 0310 Course Description_Spring 2022 (1).pdf"
## [188] "CHEM 0310 Course Description_Spring 2022 (2).pdf"
## [189] "CHEM 0310 Course Description_Spring 2022.pdf"
## [190] "Chem 0310_Feel Good Exam_Spring 2022 (1).docx"
## [191] "Chem 0310_Feel Good Exam_Spring 2022.docx"
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## [196] "Chem 0320 Practice Exam 1G.pdf"
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## [201] "Chem 0320 Synthetic Strategies- Manipulating Activating-Deactivating Groups.pdf"
## [202] "Chem 345 Discussion Problem Set 03.pdf"
## [203] "CHEM0310_Problem Set 1_Spring 2022 (1).pdf"
## [204] "CHEM0310_Problem Set 1_Spring 2022.pdf"
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## [211] "CHEM0310_Problem Set 7_Spring 2022.pdf"
## [212] "CHEM0310_Problem Set 8_Spring 2022.pdf"
## [213] "CHEM0310_Study Guide 1_Spring 2022.pdf"
## [214] "CHEM0310_Study Guide 2_Spring 2022.pdf"
## [215] "Chem2LabFinal (1).pdf"
## [216] "ChemDraw_QUICK_START_Activation_Guide(1) (1).pdf"
## [217] "ChemDraw_QUICK_START_Activation_Guide(1).pdf"
## [218] "classes_and_objects (1).py"
## [219] "classes_and_objects.py"
## [220] "Classes+and+Objects+in+Python.ipynb"
## [221] "Classwork Handout-Plots-Graphs Tomato Growth-Harvest_Data.xlsx"
## [222] "cluster_analysis_portfolio.Rmd"
## [223] "CODE_CHECKPOINT-first_rstudio_script.R"
## [224] "code_checkpoint_vcfR.Rmd"
## [225] "Colin Graduation-20210610T235014Z-001.zip"
## [226] "Colin Graduation-20210610T235014Z-002.zip"
## [227] "CompBio Tracker (1).pdf"
## [228] "CompBio Tracker.pdf"
## [229] "cos18.0.1.exe"
## [230] "costs.txt"
## [231] "CountryA.txt"
## [232] "CountryB.txt"
## [233] "Coursicle - Default Schedule.png"
## [234] "cover_jonah_langella (1).docx"
## [235] "cover_jonah_langella.docx"
## [236] "CS0011_Project1_Lab1.pdf"
## [237] "CS0011_Project1_Lab3_2221.pdf"
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## [239] "Cupers+Meier - Infrastructure JSAH 2020.pdf"
## [240] "D and E Handout 6 - Business Models and Business Plans.pdf"
## [241] "Data_VLOOKUP.xlsx"
## [242] "Data826.txt"
## [243] "dataset1.txt"
## [244] "dataset2.txt"
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## [246] "David-Sanchez.vcf"
## [247] "DE 3_Ideation and prototype.docx"
## [248] "DE 4_Presentations.pdf"
## [249] "DE 7_Business pitch instructions_c19.pdf"
## [250] "DE 7_Business pitch reflection instructions (1).pdf"
## [251] "DE 7_Business pitch reflection instructions.pdf"
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## [253] "desktop.ini"
## [254] "detailxls.zip"
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## [260] "DiscordSetup (3).exe"
## [261] "DiscordSetup.exe"
## [262] "doc_809d96a8-4bab-4535-a3f8-f748eb8e0993.pdf"
## [263] "Download entire ENGCMP syllabus here (1).docx"
## [264] "Download entire ENGCMP syllabus here.docx"
## [265] "download jawn.pdf"
## [266] "DraftKings SB PA Player Location Check (1).exe"
## [267] "DraftKings SB PA Player Location Check (2).exe"
## [268] "DraftKings SB PA Player Location Check.exe"
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## [281] "ENGCMP 0210__Format Specifications for Assignments 3, 4, 5_2020_2211.docx"
## [282] "ENGCMP 0210_Assignment 2_SSOE and Me_Fall 2020_2211.docx"
## [283] "ENGCMP 0210_Assignment 3_Engineering And Me_2020_2211.docx"
## [284] "ENGCMP 0210_Assignment 4_ENGINEERING, ETHICS, AND ME_2020_2211 (1).docx"
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## [288] "ENGCMP 0210_Assignment 4_ENGINEERING, ETHICS, AND ME_2020_2211.docx"
## [289] "ENGCMP 0210_Evaluation Abbreviations_2020_2211.docx"
## [290] "ENGCMP 0210_FORMAT SAMPLE_2020.docx"
## [291] "ENGCMP 0210_FORMAT SPECIFICATIONS_Assignment 2_SSOE & Me_2020_2211 (1).docx"
## [292] "ENGCMP 0210_FORMAT SPECIFICATIONS_Assignment 2_SSOE & Me_2020_2211 (2).docx"
## [293] "ENGCMP 0210_FORMAT SPECIFICATIONS_Assignment 2_SSOE & Me_2020_2211 (3).docx"
## [294] "ENGCMP 0210_FORMAT SPECIFICATIONS_Assignment 2_SSOE & Me_2020_2211.docx"
## [295] "ENGCMP 0412___Format Requirements for Annot. Outline & FYEC Paper_2021_2214.docx"
## [296] "ENGCMP 0412__Format Requirements for Annot. Outline & FYEC Paper_2021_2214.docx"
## [297] "ENGCMP 0412_Assignmemt 1_FYEC Team Prelim Proposal_2021 (1).docx"
## [298] "ENGCMP 0412_Assignmemt 1_FYEC Team Prelim Proposal_2021 (2).docx"
## [299] "ENGCMP 0412_Assignmemt 1_FYEC Team Prelim Proposal_2021 .docx"
## [300] "ENGCMP 0412_FYEC Call for Papers_2021-2214 (1).docx"
## [301] "ENGCMP 0412_FYEC Call for Papers_2021-2214.docx"
## [302] "enginedata.csv"
## [303] "engineering-graph-paper-bw.pdf"
## [304] "EntertheMatrix.java"
## [305] "EpicInstaller-13.0.0.msi"
## [306] "Eq1.txt"
## [307] "eqns_to_solve.txt"
## [308] "eqns1.txt"
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## [310] "Essay_topic_2021S.pdf"
## [311] "ethics, engineering, and me REVISION FINAL (1).docx"
## [312] "ethics, engineering, and me REVISION FINAL petra.docx"
## [313] "ethics, engineering, and me REVISION FINAL.docx"
## [314] "ethics, engineering, and me. (1).docx"
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## [316] "Exam1.pdf"
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## [318] "Exam2SampleProblems_Calc3_Fall2021 (1).pdf"
## [319] "Exam2SampleProblems_Calc3_Fall2021.pdf"
## [320] "Excel HW2.pdf"
## [321] "Excel HW4 (1).pdf"
## [322] "Excel HW4 (2).pdf"
## [323] "Excel HW4.pdf"
## [324] "Excel HW6 - view solution.pdf"
## [325] "exodus-windows-x64-22.5.10.exe"
## [326] "expiriment6_langella.pdf"
## [327] "FA22_Flowers_BIOSC 1690 Form-1cr (1).pdf"
## [328] "FA22_Flowers_BIOSC 1690 Form-1cr.pdf"
## [329] "Fall 2020 ENGR 11 course syllabus-5 (1).pdf"
## [330] "Fall 2020 ENGR 11 course syllabus-5 (2).pdf"
## [331] "Fall 2020 ENGR 11 course syllabus-5.pdf"
## [332] "Fall 2020 Excel HW5 (1).pdf"
## [333] "Fall 2020 Excel HW5 (2).pdf"
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## [335] "Fall 2020 Excel HW6.pdf"
## [336] "Fall 2020 Excel HW7.pdf"
## [337] "FALL 21 Roy 1070 GENE EXPRESSION CONTROL-ncq [Compatibility Mode].pdf"
## [338] "FALL 21 Roy Gene Manipulation-ncq [Compatibility Mode].pdf"
## [339] "feature_engineering.Rmd"
## [340] "Figure_ Introduction (1).pdf"
## [341] "Figure_ Introduction.pdf"
## [342] "fiji-win64"
## [343] "fiji-win64.zip"
## [344] "FileReadSample.java"
## [345] "FiletoArray.java"
## [346] "Fillable Semester Planner_1.2022.pdf"
## [347] "Final_Test_3_2021.pdf"
## [348] "FinalExam.pdf"
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## [350] "Flex Pitt Provisions.pdf"
## [351] "Flow chart assignment_Flowers_F21-1.pptx"
## [352] "Flowers-Getting to Know You PPT Template.pptx"
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## [359] "Fundamentals of Physics Extended by David Halliday, Robert Resnick, Jearl Walker (z-lib.org).pdf"
## [360] "Fundamentals of Physics, Extended, 11th edition-978-1-119-46013-8.pdf"
## [361] "FW____SAVE_FOR_YOUR_FILES___--_UPMC_MERCY_2023_BLS_&_ACLS_eFlyers_with_Embedded_Self-enroll_Deep_Links_for_Easy_Staff_Access.zip"
## [362] "ge210-setup.exe"
## [363] "geany-1.37.1_setup.exe"
## [364] "Gel Electrophoresis flowchart_Student_Flowers_F21.pptx"
## [365] "Ger1004 Referat.ppt"
## [366] "GER1004_Unterrichtsplan_2021 (1).pdf"
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## [371] "GoogleEarthProSetup.exe"
## [372] "Group B Data.xlsx"
## [373] "Hist_data.txt"
## [374] "Histograms_InClass.xlsx"
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## [743] "x_y_data.txt" # todoIf you have lots of files in the working directory, you can search for the file specifically with list.files(pattern = “vcf”)
# Run list.files() with pattern = "vcf
# todo
list.files(pattern = "vcf")## [1] "10.34543678-34783678.ALL.chr10_GRCh38.genotypes.20170504.vcf.gz"
## [2] "ALL.chr10_GRCh38.genotypes.20170504.vcf.gz"
## [3] "all_loci.vcf"
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## [6] "vcfR_test.vcf"
## [7] "vcfR_test.vcf.gz"SNP data is often stored in Variant Call Format (VCF) files that are organized differently than normal R data. When SNP data is analyzed in R, such as by doing PCA or cluster analysis, the SNPs are usually the features (variables) and each row is a sample (such as a person, or other organism). VCF files, however, are organized with SNPs in rows and samples in columns.
Changing how data is arranged is called reshaping. Reshaping can take different forms. In this case we need to flip the orientation of the data so that the rows, SNPS, become the columns.
In R we can flip the orientation of matrix or dataframe using
t() operation, which stands for transpose.
The transpose of a dataset takes each row and makes it into a column.
For vcf data, this means that the SNPs in rows can be made into
columns.
The example below will illustrate the general principle of transposition of data. First, let’s make two vectors of data in vcf-like format, with genotypes expressed as “A|A”.
# Add the c() function to make
## vectors containing SNP genotypes
SNP01 <- c("A|A","A|A","A|A","A|A") # TODO
SNP02 <- c("G|G","G|G","G|G","G|G")Now let’s make a matrix with rbind()
# add the rbind() function
## to combine the vectors into a dataframe
my_matrix <- rbind(SNP01, SNP02) # TODOSince this is representing a vcf file, the rows will be SNPS and the
columns will be samples. I’ll name the columns with
colnames().
# add the colnames() function around
## the my_matrix object to
## rename it
colnames(my_matrix) <- c("sample1", # TODO
"sample2",
"sample3",
"sample4")We now have a matrix in the general form of a vcf file
# add the my_matrix object to the chunk so
## its contents are shown
my_matrix## sample1 sample2 sample3 sample4
## SNP01 "A|A" "A|A" "A|A" "A|A"
## SNP02 "G|G" "G|G" "G|G" "G|G" # TODOThe t() function will re-orient our matrix for us so
that SNPs are in columns and samples are in rows.
# add the t() function to transpose
## the matrix
t(my_matrix) # TODO## SNP01 SNP02
## sample1 "A|A" "G|G"
## sample2 "A|A" "G|G"
## sample3 "A|A" "G|G"
## sample4 "A|A" "G|G"We can save the transposed output to a new matrix.
# add the t() function and assign
## the output to an object called
## my_matrix_t
my_matrix_t <- (my_matrix) # TODOWe can do this in R with dataframes also:
# add the data.frame() function to
## turn my_matrix into a dataframe
## and assign it to an object called my_df
my_df <- data.frame(my_matrix) # TODOAgain, t() flips the dataframe for us:
# add the t() function to show the flipped
## dataframe
t(my_df) # TODO## SNP01 SNP02
## sample1 "A|A" "G|G"
## sample2 "A|A" "G|G"
## sample3 "A|A" "G|G"
## sample4 "A|A" "G|G"A typical VCF file can be found in the file
all_loci.vcf. (Note that this file is NOT compressed and so
has an extension of .vcf, not .vcf.gz). Load
the data into an object called bird_snps using the function
vcfR::read.vcfR().
NOTE - before you begin, make sure your WORKING DIRECTORY is set to the location of the .vcf file being used.
# Load the data with vcfR::read.vcfR()
# into an object called bird_snps
bird_snps <- 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("If this didn't work, you may not have set your working directory to the location of the vcf file")## Warning: If this didn't work, you may not have set your working directory to the
## location of the vcf fileMake sure that at the bottom of the output in the console it says “Processed variant: 1929”.
Call head on the bird_snps object. You should be able to identify the metadata (at the top) and be able to see how samples are organized in rows.
# run head() on bird_snps
head(bird_snps) # TODO## [1] "***** Object of class 'vcfR' *****"
## [1] "***** Meta section *****"
## [1] "##fileformat=VCFv4.0"
## [1] "##fileDate=20160506"
## [1] "##source=\"Stacks v1.20\""
## [1] "##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">"
## [1] "##INFO=<ID=AF,Number=.,Type=Float,Description=\"Allele Frequency\">"
## [1] "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">"
## [1] "First 6 rows."
## [1]
## [1] "***** Fixed section *****"
## CHROM POS ID REF ALT QUAL FILTER
## [1,] "un" "1478" "17" "C" "A" NA "PASS"
## [2,] "un" "1479" "17" "A" "G" NA "PASS"
## [3,] "un" "1723" "20" "C" "T" NA "PASS"
## [4,] "un" "1948" "22" "C" "A" NA "PASS"
## [5,] "un" "1972" "22" "C" "T" NA "PASS"
## [6,] "un" "2299" "26" "C" "T" NA "PASS"
## [1]
## [1] "***** Genotype section *****"
## FORMAT sample_ACAAA_Nel3 sample_ACAGTG_Nel5
## [1,] "GT:DP:GL" "1/0:344:.,-359.6,." "1/0:265:.,-273.8,."
## [2,] "GT:DP:GL" "0/1:344:.,-359.6,." "0/1:265:.,-273.8,."
## [3,] "GT:DP:GL" "0/0:254:.,352.119,." "0/0:267:.,370.141,."
## [4,] "GT:DP:GL" "0/0:332:.,460.25,." "0/0:339:.,469.954,."
## [5,] "GT:DP:GL" "0/0:332:.,431.419,." "0/0:339:.,454.108,."
## [6,] "GT:DP:GL" "0/0:421:.,553.847,." "0/0:412:.,540.081,."
## sample_AGCAT_Nel8 sample_ATGAAAC_Nel10 sample_ATGAAAC_Nel15
## [1,] "0/0:252:.,349.346,." "0/0:253:.,350.732,." "0/0:260:.,360.437,."
## [2,] "0/0:252:.,349.346,." "0/0:253:.,350.732,." "0/0:260:.,360.437,."
## [3,] "0/0:373:.,517.088,." "0/0:222:.,307.757,." "0/0:298:.,413.116,."
## [4,] "0/0:288:.,399.253,." "0/0:232:.,321.62,." "0/0:342:.,474.113,."
## [5,] "0/0:288:.,399.253,." "0/0:232:.,321.62,." "0/0:342:.,474.113,."
## [6,] "0/0:444:.,615.515,." "0/0:377:.,522.633,." "0/0:379:.,525.406,."
## [1] "First 6 columns only."
## [1]
## [1] "Unique GT formats:"
## [1] "GT:DP:GL"
## [1]We can view just the meta data like this:
bird_snps@meta## [1] "##fileformat=VCFv4.0"
## [2] "##fileDate=20160506"
## [3] "##source=\"Stacks v1.20\""
## [4] "##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">"
## [5] "##INFO=<ID=AF,Number=.,Type=Float,Description=\"Allele Frequency\">"
## [6] "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">"
## [7] "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">"
## [8] "##FORMAT=<ID=GL,Number=.,Type=Float,Description=\"Genotype Likelihood\">"(Don’t worry about what the “at” symbol is using - this is a somewhat less common R syntax).
We can get a snapshot of the samples like this:
bird_snps@gt[1:10, 1:3]## FORMAT sample_ACAAA_Nel3 sample_ACAGTG_Nel5
## [1,] "GT:DP:GL" "1/0:344:.,-359.6,." "1/0:265:.,-273.8,."
## [2,] "GT:DP:GL" "0/1:344:.,-359.6,." "0/1:265:.,-273.8,."
## [3,] "GT:DP:GL" "0/0:254:.,352.119,." "0/0:267:.,370.141,."
## [4,] "GT:DP:GL" "0/0:332:.,460.25,." "0/0:339:.,469.954,."
## [5,] "GT:DP:GL" "0/0:332:.,431.419,." "0/0:339:.,454.108,."
## [6,] "GT:DP:GL" "0/0:421:.,553.847,." "0/0:412:.,540.081,."
## [7,] "GT:DP:GL" "0/0:421:.,583.63,." "0/0:412:.,571.153,."
## [8,] "GT:DP:GL" "0/0:421:.,583.63,." "0/0:412:.,571.153,."
## [9,] "GT:DP:GL" "0/0:528:.,731.963,." "0/0:301:.,417.275,."
## [10,] "GT:DP:GL" "0/0:253:.,350.732,." "0/0:248:.,343.801,."Each row is a SNP and each column is a sample (a bird in this case.)
We extract genotype scores using vcfR::extract.gt(). You
need to be familiar with this command, but I’ll give you the code to do
this on an exam.
# Add vcfR::extract.gt() to extract the
## numeric scores
bird_snps_num <- extract.gt(bird_snps, # TODO
element = "GT",
IDtoRowNames = F,
as.numeric = T,
convertNA = T)We now have just the numeric data that would go into an analysis such as PCA.
The sample names are REALLY long so its hard to display in a compact
way. The code below will make this a a little easier to see using the
regular expression gsub().
colnames(bird_snps_num) <- gsub("sample_", "",
colnames(bird_snps_num))
colnames(bird_snps_num) <- gsub("_", "",
colnames(bird_snps_num))We can see that the matrix just contains numeric genotype scores of 0, 1 or 2.
Here’s a small view of data:
bird_snps_num[1:10, 1:4]## ACAAANel3 ACAGTGNel5 AGCATNel8 ATGAAACNel10
## [1,] 1 1 0 0
## [2,] 0 0 0 0
## [3,] 0 0 0 0
## [4,] 0 0 0 0
## [5,] 0 0 0 0
## [6,] 0 0 0 0
## [7,] 0 0 0 0
## [8,] 0 0 0 0
## [9,] 0 0 0 0
## [10,] 0 0 0 0We can call summary of a bit of the data like this:
summary(bird_snps_num[, 1:5])## ACAAANel3 ACAGTGNel5 AGCATNel8 ATGAAACNel10
## Min. :0.00000 Min. :0.00000 Min. :0.00000 Min. :0.00000
## 1st Qu.:0.00000 1st Qu.:0.00000 1st Qu.:0.00000 1st Qu.:0.00000
## Median :0.00000 Median :0.00000 Median :0.00000 Median :0.00000
## Mean :0.08574 Mean :0.07962 Mean :0.08259 Mean :0.07192
## 3rd Qu.:0.00000 3rd Qu.:0.00000 3rd Qu.:0.00000 3rd Qu.:0.00000
## Max. :1.00000 Max. :1.00000 Max. :1.00000 Max. :1.00000
## NA's :28 NA's :20 NA's :28 NA's :24
## ATGAAACNel15
## Min. :0.0000
## 1st Qu.:0.0000
## Median :0.0000
## Mean :0.0766
## 3rd Qu.:0.0000
## Max. :1.0000
## NA's :23The data are formatted as genotype scores but SNPs are in columns and
samples in row. We can reformat them using the transpose function
t().
# run t() on bird_snps_num and
## save the output to bird_snps_num_t
bird_snps_num_t <- t(bird_snps_num) # TODOWe can look at the output like this:
bird_snps_num_t[1:10, 1:4]## [,1] [,2] [,3] [,4]
## ACAAANel3 1 0 0 0
## ACAGTGNel5 1 0 0 0
## AGCATNel8 0 0 0 0
## ATGAAACNel10 0 0 0 0
## ATGAAACNel15 0 0 0 0
## CGATGTNel4 0 0 0 0
## CTAGCNel7 0 0 0 0
## CTGTANel12 0 0 0 0
## CTGTANel9 0 0 0 0
## CTTGANel2 0 0 0 0These 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
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) # TODO
# what is the remaining size of the data?
# why
(no_NAs) # TODO## [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
## [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26]
## [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] [,38]
## [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48] [,49] [,50]
## [,51] [,52] [,53] [,54] [,55] [,56] [,57] [,58] [,59] [,60] [,61] [,62]
## [,63] [,64] [,65] [,66] [,67] [,68] [,69] [,70] [,71] [,72] [,73] [,74]
## [,75] [,76] [,77] [,78] [,79] [,80] [,81] [,82] [,83] [,84] [,85] [,86]
## [,87] [,88] [,89] [,90] [,91] [,92] [,93] [,94] [,95] [,96] [,97] [,98]
## [,99] [,100] [,101] [,102] [,103] [,104] [,105] [,106] [,107] [,108]
## [,109] [,110] [,111] [,112] [,113] [,114] [,115] [,116] [,117] [,118]
## [,119] [,120] [,121] [,122] [,123] [,124] [,125] [,126] [,127] [,128]
## [,129] [,130] [,131] [,132] [,133] [,134] [,135] [,136] [,137] [,138]
## [,139] [,140] [,141] [,142] [,143] [,144] [,145] [,146] [,147] [,148]
## [,149] [,150] [,151] [,152] [,153] [,154] [,155] [,156] [,157] [,158]
## [,159] [,160] [,161] [,162] [,163] [,164] [,165] [,166] [,167] [,168]
## [,169] [,170] [,171] [,172] [,173] [,174] [,175] [,176] [,177] [,178]
## [,179] [,180] [,181] [,182] [,183] [,184] [,185] [,186] [,187] [,188]
## [,189] [,190] [,191] [,192] [,193] [,194] [,195] [,196] [,197] [,198]
## [,199] [,200] [,201] [,202] [,203] [,204] [,205] [,206] [,207] [,208]
## [,209] [,210] [,211] [,212] [,213] [,214] [,215] [,216] [,217] [,218]
## [,219] [,220] [,221] [,222] [,223] [,224] [,225] [,226] [,227] [,228]
## [,229] [,230] [,231] [,232] [,233] [,234] [,235] [,236] [,237] [,238]
## [,239] [,240] [,241] [,242] [,243] [,244] [,245] [,246] [,247] [,248]
## [,249] [,250] [,251] [,252] [,253] [,254] [,255] [,256] [,257] [,258]
## [,259] [,260] [,261] [,262] [,263] [,264] [,265] [,266] [,267] [,268]
## [,269] [,270] [,271] [,272] [,273] [,274] [,275] [,276] [,277] [,278]
## [,279] [,280] [,281] [,282] [,283] [,284] [,285] [,286] [,287] [,288]
## [,289] [,290] [,291] [,292] [,293] [,294] [,295] [,296] [,297] [,298]
## [,299] [,300] [,301] [,302] [,303] [,304] [,305] [,306] [,307] [,308]
## [,309] [,310] [,311] [,312] [,313] [,314] [,315] [,316] [,317] [,318]
## [,319] [,320] [,321] [,322] [,323] [,324] [,325] [,326] [,327] [,328]
## [,329] [,330] [,331] [,332] [,333] [,334] [,335] [,336] [,337] [,338]
## [,339] [,340] [,341] [,342] [,343] [,344] [,345] [,346] [,347] [,348]
## [,349] [,350] [,351] [,352] [,353] [,354] [,355] [,356] [,357] [,358]
## [,359] [,360] [,361] [,362] [,363] [,364] [,365] [,366] [,367] [,368]
## [,369] [,370] [,371] [,372] [,373] [,374] [,375] [,376] [,377] [,378]
## [,379] [,380] [,381] [,382] [,383] [,384] [,385] [,386] [,387] [,388]
## [,389] [,390] [,391] [,392] [,393] [,394] [,395] [,396] [,397] [,398]
## [,399] [,400] [,401] [,402] [,403] [,404] [,405] [,406] [,407] [,408]
## [,409] [,410] [,411] [,412] [,413] [,414] [,415] [,416] [,417] [,418]
## [,419] [,420] [,421] [,422] [,423] [,424] [,425] [,426] [,427] [,428]
## [,429] [,430] [,431] [,432] [,433] [,434] [,435] [,436] [,437] [,438]
## [,439] [,440] [,441] [,442] [,443] [,444] [,445] [,446] [,447] [,448]
## [,449] [,450] [,451] [,452] [,453] [,454] [,455] [,456] [,457] [,458]
## [,459] [,460] [,461] [,462] [,463] [,464] [,465] [,466] [,467] [,468]
## [,469] [,470] [,471] [,472] [,473] [,474] [,475] [,476] [,477] [,478]
## [,479] [,480] [,481] [,482] [,483] [,484] [,485] [,486] [,487] [,488]
## [,489] [,490] [,491] [,492] [,493] [,494] [,495] [,496] [,497] [,498]
## [,499] [,500] [,501] [,502] [,503] [,504] [,505] [,506] [,507] [,508]
## [,509] [,510] [,511] [,512] [,513] [,514] [,515] [,516] [,517] [,518]
## [,519] [,520] [,521] [,522] [,523] [,524] [,525] [,526] [,527] [,528]
## [,529] [,530] [,531] [,532] [,533] [,534] [,535] [,536] [,537] [,538]
## [,539] [,540] [,541] [,542] [,543] [,544] [,545] [,546] [,547] [,548]
## [,549] [,550] [,551] [,552] [,553] [,554] [,555] [,556] [,557] [,558]
## [,559] [,560] [,561] [,562] [,563] [,564] [,565] [,566] [,567] [,568]
## [,569] [,570] [,571] [,572] [,573] [,574] [,575] [,576] [,577] [,578]
## [,579] [,580] [,581] [,582] [,583] [,584] [,585] [,586] [,587] [,588]
## [,589] [,590] [,591] [,592] [,593] [,594] [,595] [,596] [,597] [,598]
## [,599] [,600] [,601] [,602] [,603] [,604] [,605] [,606] [,607] [,608]
## [,609] [,610] [,611] [,612] [,613] [,614] [,615] [,616] [,617] [,618]
## [,619] [,620] [,621] [,622] [,623] [,624] [,625] [,626] [,627] [,628]
## [,629] [,630] [,631] [,632] [,633] [,634] [,635] [,636] [,637] [,638]
## [,639] [,640] [,641] [,642] [,643] [,644] [,645] [,646] [,647] [,648]
## [,649] [,650] [,651] [,652] [,653] [,654] [,655] [,656] [,657] [,658]
## [,659] [,660] [,661] [,662] [,663] [,664] [,665] [,666] [,667] [,668]
## [,669] [,670] [,671] [,672] [,673] [,674] [,675] [,676] [,677] [,678]
## [,679] [,680] [,681] [,682] [,683] [,684] [,685] [,686] [,687] [,688]
## [,689] [,690] [,691] [,692] [,693] [,694] [,695] [,696] [,697] [,698]
## [,699] [,700] [,701] [,702] [,703] [,704] [,705] [,706] [,707] [,708]
## [,709] [,710] [,711] [,712] [,713] [,714] [,715] [,716] [,717] [,718]
## [,719] [,720] [,721] [,722] [,723] [,724] [,725] [,726] [,727] [,728]
## [,729] [,730] [,731] [,732] [,733] [,734] [,735] [,736] [,737] [,738]
## [,739] [,740] [,741] [,742] [,743] [,744] [,745] [,746] [,747] [,748]
## [,749] [,750] [,751] [,752] [,753] [,754] [,755] [,756] [,757] [,758]
## [,759] [,760] [,761] [,762] [,763] [,764] [,765] [,766] [,767] [,768]
## [,769] [,770] [,771] [,772] [,773] [,774] [,775] [,776] [,777] [,778]
## [,779] [,780] [,781] [,782] [,783] [,784] [,785] [,786] [,787] [,788]
## [,789] [,790] [,791] [,792] [,793] [,794] [,795] [,796] [,797] [,798]
## [,799] [,800] [,801] [,802] [,803] [,804] [,805] [,806] [,807] [,808]
## [,809] [,810] [,811] [,812] [,813] [,814] [,815] [,816] [,817] [,818]
## [,819] [,820] [,821] [,822] [,823] [,824] [,825] [,826] [,827] [,828]
## [,829] [,830] [,831] [,832] [,833] [,834] [,835] [,836] [,837] [,838]
## [,839] [,840] [,841] [,842] [,843] [,844] [,845] [,846] [,847] [,848]
## [,849] [,850] [,851] [,852] [,853] [,854] [,855] [,856] [,857] [,858]
## [,859] [,860] [,861] [,862] [,863] [,864] [,865] [,866] [,867] [,868]
## [,869] [,870] [,871] [,872] [,873] [,874] [,875] [,876] [,877] [,878]
## [,879] [,880] [,881] [,882] [,883] [,884] [,885] [,886] [,887] [,888]
## [,889] [,890] [,891] [,892] [,893] [,894] [,895] [,896] [,897] [,898]
## [,899] [,900] [,901] [,902] [,903] [,904] [,905] [,906] [,907] [,908]
## [,909] [,910] [,911] [,912] [,913] [,914] [,915] [,916] [,917] [,918]
## [,919] [,920] [,921] [,922] [,923] [,924] [,925] [,926] [,927] [,928]
## [,929] [,930] [,931] [,932] [,933] [,934] [,935] [,936] [,937] [,938]
## [,939] [,940] [,941] [,942] [,943] [,944] [,945] [,946] [,947] [,948]
## [,949] [,950] [,951] [,952] [,953] [,954] [,955] [,956] [,957] [,958]
## [,959] [,960] [,961] [,962] [,963] [,964] [,965] [,966] [,967] [,968]
## [,969] [,970] [,971] [,972] [,973] [,974] [,975] [,976] [,977] [,978]
## [,979] [,980] [,981] [,982] [,983] [,984] [,985] [,986] [,987] [,988]
## [,989] [,990] [,991] [,992] [,993] [,994] [,995] [,996] [,997] [,998]
## [,999] [,1000] [,1001] [,1002] [,1003] [,1004] [,1005] [,1006] [,1007]
## [,1008] [,1009] [,1010] [,1011] [,1012] [,1013] [,1014] [,1015] [,1016]
## [,1017] [,1018] [,1019] [,1020] [,1021] [,1022] [,1023] [,1024] [,1025]
## [,1026] [,1027] [,1028] [,1029] [,1030] [,1031] [,1032] [,1033] [,1034]
## [,1035] [,1036] [,1037] [,1038] [,1039] [,1040] [,1041] [,1042] [,1043]
## [,1044] [,1045] [,1046] [,1047] [,1048] [,1049] [,1050] [,1051] [,1052]
## [,1053] [,1054] [,1055] [,1056] [,1057] [,1058] [,1059] [,1060] [,1061]
## [,1062] [,1063] [,1064] [,1065] [,1066] [,1067] [,1068] [,1069] [,1070]
## [,1071] [,1072] [,1073] [,1074] [,1075] [,1076] [,1077] [,1078] [,1079]
## [,1080] [,1081] [,1082] [,1083] [,1084] [,1085] [,1086] [,1087] [,1088]
## [,1089] [,1090] [,1091] [,1092] [,1093] [,1094] [,1095] [,1096] [,1097]
## [,1098] [,1099] [,1100] [,1101] [,1102] [,1103] [,1104] [,1105] [,1106]
## [,1107] [,1108] [,1109] [,1110] [,1111] [,1112] [,1113] [,1114] [,1115]
## [,1116] [,1117] [,1118] [,1119] [,1120] [,1121] [,1122] [,1123] [,1124]
## [,1125] [,1126] [,1127] [,1128] [,1129] [,1130] [,1131] [,1132] [,1133]
## [,1134] [,1135] [,1136] [,1137] [,1138] [,1139] [,1140] [,1141] [,1142]
## [,1143] [,1144] [,1145] [,1146] [,1147] [,1148] [,1149] [,1150] [,1151]
## [,1152] [,1153] [,1154] [,1155] [,1156] [,1157] [,1158] [,1159] [,1160]
## [,1161] [,1162] [,1163] [,1164] [,1165] [,1166] [,1167] [,1168] [,1169]
## [,1170] [,1171] [,1172] [,1173] [,1174] [,1175] [,1176] [,1177] [,1178]
## [,1179] [,1180] [,1181] [,1182] [,1183] [,1184] [,1185] [,1186] [,1187]
## [,1188] [,1189] [,1190] [,1191] [,1192] [,1193] [,1194] [,1195] [,1196]
## [,1197] [,1198] [,1199] [,1200] [,1201] [,1202] [,1203] [,1204] [,1205]
## [,1206] [,1207] [,1208] [,1209] [,1210] [,1211] [,1212] [,1213] [,1214]
## [,1215] [,1216] [,1217] [,1218] [,1219] [,1220] [,1221] [,1222] [,1223]
## [,1224] [,1225] [,1226] [,1227] [,1228] [,1229] [,1230] [,1231] [,1232]
## [,1233] [,1234] [,1235] [,1236] [,1237] [,1238] [,1239] [,1240] [,1241]
## [,1242] [,1243] [,1244] [,1245] [,1246] [,1247] [,1248] [,1249] [,1250]
## [,1251] [,1252] [,1253] [,1254] [,1255] [,1256] [,1257] [,1258] [,1259]
## [,1260] [,1261] [,1262] [,1263] [,1264] [,1265] [,1266] [,1267] [,1268]
## [,1269] [,1270] [,1271] [,1272] [,1273] [,1274] [,1275] [,1276] [,1277]
## [,1278] [,1279] [,1280] [,1281] [,1282] [,1283] [,1284] [,1285] [,1286]
## [,1287] [,1288] [,1289] [,1290] [,1291] [,1292] [,1293] [,1294] [,1295]
## [,1296] [,1297] [,1298] [,1299] [,1300] [,1301] [,1302] [,1303] [,1304]
## [,1305] [,1306] [,1307] [,1308] [,1309] [,1310] [,1311] [,1312] [,1313]
## [,1314] [,1315] [,1316] [,1317] [,1318] [,1319] [,1320] [,1321] [,1322]
## [,1323] [,1324] [,1325] [,1326] [,1327] [,1328] [,1329] [,1330] [,1331]
## [,1332] [,1333] [,1334] [,1335] [,1336] [,1337] [,1338] [,1339] [,1340]
## [,1341] [,1342] [,1343] [,1344] [,1345] [,1346] [,1347] [,1348] [,1349]
## [,1350] [,1351] [,1352] [,1353] [,1354] [,1355] [,1356] [,1357] [,1358]
## [,1359] [,1360] [,1361] [,1362] [,1363] [,1364] [,1365] [,1366] [,1367]
## [,1368] [,1369] [,1370] [,1371] [,1372] [,1373] [,1374] [,1375] [,1376]
## [,1377] [,1378] [,1379] [,1380] [,1381] [,1382] [,1383] [,1384] [,1385]
## [,1386] [,1387] [,1388] [,1389] [,1390] [,1391] [,1392] [,1393] [,1394]
## [,1395] [,1396] [,1397] [,1398] [,1399] [,1400] [,1401] [,1402] [,1403]
## [,1404] [,1405] [,1406] [,1407] [,1408] [,1409] [,1410] [,1411] [,1412]
## [,1413] [,1414] [,1415] [,1416] [,1417] [,1418] [,1419] [,1420] [,1421]
## [,1422] [,1423] [,1424] [,1425] [,1426] [,1427] [,1428] [,1429] [,1430]
## [,1431] [,1432] [,1433] [,1434] [,1435] [,1436] [,1437] [,1438] [,1439]
## [,1440] [,1441] [,1442] [,1443] [,1444] [,1445] [,1446] [,1447] [,1448]
## [,1449] [,1450] [,1451] [,1452] [,1453] [,1454] [,1455] [,1456] [,1457]
## [,1458] [,1459] [,1460] [,1461] [,1462] [,1463] [,1464] [,1465] [,1466]
## [,1467] [,1468] [,1469] [,1470] [,1471] [,1472] [,1473] [,1474] [,1475]
## [,1476] [,1477] [,1478] [,1479] [,1480] [,1481] [,1482] [,1483] [,1484]
## [,1485] [,1486] [,1487] [,1488] [,1489] [,1490] [,1491] [,1492] [,1493]
## [,1494] [,1495] [,1496] [,1497] [,1498] [,1499] [,1500] [,1501] [,1502]
## [,1503] [,1504] [,1505] [,1506] [,1507] [,1508] [,1509] [,1510] [,1511]
## [,1512] [,1513] [,1514] [,1515] [,1516] [,1517] [,1518] [,1519] [,1520]
## [,1521] [,1522] [,1523] [,1524] [,1525] [,1526] [,1527] [,1528] [,1529]
## [,1530] [,1531] [,1532] [,1533] [,1534] [,1535] [,1536] [,1537] [,1538]
## [,1539] [,1540] [,1541] [,1542] [,1543] [,1544] [,1545] [,1546] [,1547]
## [,1548] [,1549] [,1550] [,1551] [,1552] [,1553] [,1554] [,1555] [,1556]
## [,1557] [,1558] [,1559] [,1560] [,1561] [,1562] [,1563] [,1564] [,1565]
## [,1566] [,1567] [,1568] [,1569] [,1570] [,1571] [,1572] [,1573] [,1574]
## [,1575] [,1576] [,1577] [,1578] [,1579] [,1580] [,1581] [,1582] [,1583]
## [,1584] [,1585] [,1586] [,1587] [,1588] [,1589] [,1590] [,1591] [,1592]
## [,1593] [,1594] [,1595] [,1596] [,1597] [,1598] [,1599] [,1600] [,1601]
## [,1602] [,1603] [,1604] [,1605] [,1606] [,1607] [,1608] [,1609] [,1610]
## [,1611] [,1612] [,1613] [,1614] [,1615] [,1616] [,1617] [,1618] [,1619]
## [,1620] [,1621] [,1622] [,1623] [,1624] [,1625] [,1626] [,1627] [,1628]
## [,1629] [,1630] [,1631] [,1632] [,1633] [,1634] [,1635] [,1636] [,1637]
## [,1638] [,1639] [,1640] [,1641] [,1642] [,1643] [,1644] [,1645] [,1646]
## [,1647] [,1648] [,1649] [,1650] [,1651] [,1652] [,1653] [,1654] [,1655]
## [,1656] [,1657] [,1658] [,1659] [,1660] [,1661] [,1662] [,1663] [,1664]
## [,1665] [,1666] [,1667] [,1668] [,1669] [,1670] [,1671] [,1672] [,1673]
## [,1674] [,1675] [,1676] [,1677] [,1678] [,1679] [,1680] [,1681] [,1682]
## [,1683] [,1684] [,1685] [,1686] [,1687] [,1688] [,1689] [,1690] [,1691]
## [,1692] [,1693] [,1694] [,1695] [,1696] [,1697] [,1698] [,1699] [,1700]
## [,1701] [,1702] [,1703] [,1704] [,1705] [,1706] [,1707] [,1708] [,1709]
## [,1710] [,1711] [,1712] [,1713] [,1714] [,1715] [,1716] [,1717] [,1718]
## [,1719] [,1720] [,1721] [,1722] [,1723] [,1724] [,1725] [,1726] [,1727]
## [,1728] [,1729] [,1730] [,1731] [,1732] [,1733] [,1734] [,1735] [,1736]
## [,1737] [,1738] [,1739] [,1740] [,1741] [,1742] [,1743] [,1744] [,1745]
## [,1746] [,1747] [,1748] [,1749] [,1750] [,1751] [,1752] [,1753] [,1754]
## [,1755] [,1756] [,1757] [,1758] [,1759] [,1760] [,1761] [,1762] [,1763]
## [,1764] [,1765] [,1766] [,1767] [,1768] [,1769] [,1770] [,1771] [,1772]
## [,1773] [,1774] [,1775] [,1776] [,1777] [,1778] [,1779] [,1780] [,1781]
## [,1782] [,1783] [,1784] [,1785] [,1786] [,1787] [,1788] [,1789] [,1790]
## [,1791] [,1792] [,1793] [,1794] [,1795] [,1796] [,1797] [,1798] [,1799]
## [,1800] [,1801] [,1802] [,1803] [,1804] [,1805] [,1806] [,1807] [,1808]
## [,1809] [,1810] [,1811] [,1812] [,1813] [,1814] [,1815] [,1816] [,1817]
## [,1818] [,1819] [,1820] [,1821] [,1822] [,1823] [,1824] [,1825] [,1826]
## [,1827] [,1828] [,1829] [,1830] [,1831] [,1832] [,1833] [,1834] [,1835]
## [,1836] [,1837] [,1838] [,1839] [,1840] [,1841] [,1842] [,1843] [,1844]
## [,1845] [,1846] [,1847] [,1848] [,1849] [,1850] [,1851] [,1852] [,1853]
## [,1854] [,1855] [,1856] [,1857] [,1858] [,1859] [,1860] [,1861] [,1862]
## [,1863] [,1864] [,1865] [,1866] [,1867] [,1868] [,1869] [,1870] [,1871]
## [,1872] [,1873] [,1874] [,1875] [,1876] [,1877] [,1878] [,1879] [,1880]
## [,1881] [,1882] [,1883] [,1884] [,1885] [,1886] [,1887] [,1888] [,1889]
## [,1890] [,1891] [,1892] [,1893] [,1894] [,1895] [,1896] [,1897] [,1898]
## [,1899] [,1900] [,1901] [,1902] [,1903] [,1904] [,1905] [,1906] [,1907]
## [,1908] [,1909] [,1910] [,1911] [,1912] [,1913] [,1914] [,1915] [,1916]
## [,1917] [,1918] [,1919] [,1920] [,1921] [,1922] [,1923] [,1924] [,1925]
## [,1926] [,1927] [,1928] [,1929]
## attr(,"na.action")
## AAAAGTTSub15 CGATGTSub6 CTAGCSub3 CTTGCTTSub8 GCCAATSub4 GTATTSub12
## 31 36 37 39 41 43
## ACAGTGCau2 ATGAAACCau12 CTGTACau8 GAATTCACau10 AGCCCSub11 CTTGCTTSub14
## 45 50 52 53 35 38
## CTAGCCau5 ATCACGDiv1 AGCATNel8 TTAGGCAlt2 TCACCCau4 AAAAGTTDiv13
## 51 63 3 28 56 59
## AGCATDiv11 GTATTDiv10 ACAAASub1 ATGAAACDiv8 GTATTDiv7 ACAGTGCau3
## 61 69 32 64 70 46
## AGCCCCau7 GGACCTACau13 CTTGANel2 CTTGCTTDiv15 TGACCASub2 CGATGTNel4
## 49 54 10 68 44 6
## GCCAATAlt9 CTAGCDiv2 ACTATDiv14 TGACCADiv5 AAAAGTTDiv12 GAATTCASub9
## 27 66 60 71 58 40
## ACTATCau11 ATCACGAlt5 AGCCCDiv9 TCACCNel6 AGCCCAlt13 AGCATSub13
## 47 20 62 14 19 34
## TCACCCau1 CTAGCNel7 ACAAAAlt11 CTGTAAlt14 CGATGTDiv3 CGATGTAlt1
## 55 7 17 23 65 22
## CTGTANel12 TGACCANel1 GAATTCAAlt15 GGACCTASub10 CTTGADiv6 ACTATCau9
## 8 15 25 42 67 48
## ATGAAACNel15 GGACCTANel13 GTATTNel14 ACAGTGNel5 ATCACGAlt7 ACTATSub7
## 5 12 13 2 21 33
## TTAGGCDiv4 ATGAAACNel10 GGACCTANel11 ACAGTGAlt3 CTTGAAlt10 TGACCACau6
## 72 4 11 18 24 57
## CTGTANel9 TTAGGCAlt6 TTAGGCAlt8 ACAAANel3 GCCAATAlt4 AAAAGTTAlt12
## 9 29 30 1 26 16
## attr(,"class")
## [1] "omit"