Worked Example: PCA on SNPs data from a vcf file Part 1 - Data Preparation
2022-11-19
Introduction
In this worked example you will replicate a PCA on a published dataset.
The example is split into 2 Parts:
- Part 1: Data Preparation (this file)
- Part 2: Data analysis with PCA
In this Data Preparation phase, you will do the following things:
- Load the SNP genotypes in .vcf format
(
vcfR::read.vcfR()) - Extract the genotypes into an R-compatible format
(
vcfR::extract.gt()) - Rotate the data into the standard R analysis format
(
t()) - Remove individuals (rows) from the data set that have >50% NAs (using a function I wrote)
- Remove SNPs (columns) that are fixed
- Impute remaining NAs (using a
for()loop) - Save the prepared data as a
.csvfile for the next step (write.csv())
Biological background
This worked example is based on a paper in the journal Molecular Ecology from 2017 by Jennifer Walsh titled Subspecies delineation amid phenotypic, geographic and genetic discordance in a songbird.
The study investigated variation between two bird species in the genus Ammodramus: A. nenlsoni and A. caudacutus.
The species A. nenlsoni has been divided into 3 sub-species: A. n. nenlsoni, A.n. alterus, and A n. subvirgatus. The other species, A. caudacutus, has been divided into two subspecies, A.c. caudacutus and A.c. diversus.
The purpose of this study was to investigate to what extent these five subspecies recognized by taxonomists are supported by genetic data. The author’s collected DNA from 75 birds (15 per subspecies) and genotyped 1929 SNPs. They then analyzed the data with Principal Components Analysis (PCA), among other genetic analyzes.
This tutorial will work through all of the steps necessary to re-analyze Walsh et al.s data
Tasks
In the code below all code is provided. Your tasks will be to do 2 things:
- Give a meaningful title to all sections marked “TODO: TITLE”
- Write 1 to 2 sentences describing what is being done and why in all sections marked “TODO: EXPLAIN”
Preliminaries
Load the vcfR and other packages with library().
library(vcfR) ##
## ***** *** vcfR *** *****
## This is vcfR 1.13.0
## browseVignettes('vcfR') # Documentation
## citation('vcfR') # Citation
## ***** ***** ***** *****library(vegan)## Loading required package: permute## Loading required package: lattice## This is vegan 2.6-4library(ggplot2)
library(ggpubr)Make sure that your working directory is set to the location of the
file all_loci.vcf.
getwd()## [1] "/Users/angelazhu/Downloads"list.files()## [1] "_9.9-sc-notes-ks (1).pdf"
## [2] "_9.9-sc-notes-ks.pdf"
## [3] "_Consider the Lobster_ Summary Essay.pdf"
## [4] "_Industrial_ Corn_ Analysis Essay.docx"
## [5] "_Industrial_ Corn_ Analysis Essay.pdf"
## [6] "_Industrial_ Corn_ Outline.pdf"
## [7] "_The Man_ Pop Culture Essay.docx"
## [8] "“Consider the Lobster” Summary Essay (1).pdf"
## [9] "“Consider the Lobster” Summary Essay .docx"
## [10] "“Consider the Lobster” Summary Essay .pdf"
## [11] "[别笑！我是韩语学习书].金美顺.扫描版.pdf"
## [12] "~$aoyi Zhu-RA-ApplicationSpring.docx"
## [13] "~$at1000 ch8 HW - 10e.docx"
## [14] "0120b.pdf"
## [15] "07-mean_imputation.html"
## [16] "07-mean_imputation.Rmd"
## [17] "08-PCA_worked.html"
## [18] "08-PCA_worked.Rmd"
## [19] "08.31-sc-notes-ks.pdf"
## [20] "09-PCA_worked_example-SNPs-part1.Rmd"
## [21] "1_1&2_Functions.pdf"
## [22] "1.159051856-159301856.ALL.chr1_GRCh38.genotypes.20170504 (1).vcf.gz"
## [23] "1.159051856-159301856.ALL.chr1_GRCh38.genotypes.20170504.vcf.gz"
## [24] "10.07-sc-notes-jd (1).pdf"
## [25] "10.07-sc-notes-jd.pdf"
## [26] "10.12-sc-notes-am (1).docx"
## [27] "10.12-sc-notes-am.docx"
## [28] "10.19-sc-notes-DE.docx"
## [29] "10.21-sc-notes-TFG.pdf"
## [30] "10.25-vegan_pca_with_msleep-STUDENT.Rmd"
## [31] "10.26-sc-notes-jm.docx"
## [32] "10.28-sc-notes-mf.docx"
## [33] "10.5-sc-notes-TFG.pdf"
## [34] "11.01-sc-notes-VM.docx"
## [35] "11.9-sc-notes-jm.docx"
## [36] "1260599.pdf"
## [37] "130348__omachronic__soft-1.wav"
## [38] "14-1 Colligative Properties (1).docx"
## [39] "14-1 Colligative Properties (2).docx"
## [40] "14-1 Colligative Properties.docx"
## [41] "1540_week14_PCA_SNP_workflow.pdf"
## [42] "1547850638.docx"
## [43] "1665539618.908536.jpg"
## [44] "1668975884.569569.jpg"
## [45] "17-1 Acids and Bases.docx"
## [46] "17-2 Weak Acids (1).docx"
## [47] "17-2 Weak Acids.docx"
## [48] "198841__bone666138__analog-alarm-clock.wav"
## [49] "1B6C3012-9CB4-48EE-8108-7339E59FB289.heic"
## [50] "1K67885861.pdf"
## [51] "2 TRIPLE ENTRY JOURNAL .pdf"
## [52] "200_final_ review_solutions-annotated.pdf"
## [53] "2005APStatisticsFreeResponse.doc"
## [54] "2005BAPStatisticsFreeResponse.doc"
## [55] "2015 FRQs solutions.pdf"
## [56] "20200701_15027_255985.pdf"
## [57] "20201125_15027_262997.pdf"
## [58] "20201125_15027_262998.pdf"
## [59] "21-1 Radioactivity and Nuclear Reactions i.docx"
## [60] "2224-310-Func-Grp-Lst-(from Will) (1).pdf"
## [61] "2224-310-Func-Grp-Lst-(from Will).pdf"
## [62] "2224-310-pKa Values.pdf"
## [63] "237729__flathill__rain-and-thunder-4.wav"
## [64] "2ACAE985-C951-4140-81E3-24752CC569EC_1_105_c.jpeg"
## [65] "327666__juan-merie-venter__dog-bark.wav"
## [66] "340750__soundslikewillem__05-elevator-bing.wav"
## [67] "344360__amholma__door-open-close.wav"
## [68] "346572__inspectorj__train-door-beep-b.wav"
## [69] "360cse_13.0.2250.0.exe"
## [70] "360cse_setup.exe"
## [71] "360se+5000577+n761579be99 (1).exe"
## [72] "360se+5000577+n761579be99.exe"
## [73] "360zip_v1.0.2.dmg"
## [74] "401276__inspectorj__rain-moderate-b.wav"
## [75] "466864__steinhyrningur__door-closing-door-closed.m4a"
## [76] "4kvideodownloader_4.14.3.dmg"
## [77] "5C4BC888-0766-404D-92ED-BF8E1F245EF7_1_105_c.jpeg"
## [78] "6AF00CF9-E1B9-45E4-99A7-844CB85CC74A (1).heic"
## [79] "6AF00CF9-E1B9-45E4-99A7-844CB85CC74A.heic"
## [80] "7a703ed6-cae0-4716-9e13-83350ecfe812.pdf"
## [81] "9.07-sc-notes-vm (1).docx"
## [82] "9.07-sc-notes-vm.docx"
## [83] "9.14-sc-notes-MF (1).docx"
## [84] "9.14-sc-notes-MF (2).docx"
## [85] "9.14-sc-notes-MF.docx"
## [86] "9.16-sc-notes-de-1 (1).docx"
## [87] "9.16-sc-notes-de-1.docx"
## [88] "9.21-sc-notes-jm (1).docx"
## [89] "9.21-sc-notes-jm.docx"
## [90] "9.23-sc-notes-dk-1.pdf"
## [91] "99936CA0-81ED-4108-ABB8-CE99222ACC4F.heic"
## [92] "A2.java"
## [93] "A4-FS (2).zip"
## [94] "A4-FS.zip"
## [95] "A4.java"
## [96] "A5.txt"
## [97] "Abel Alegre outline-1.docx"
## [98] "Activity 2 Watson and Crick original paper.pdf"
## [99] "admissionTicket.pdf"
## [100] "admissionTicketEZ.pdf"
## [101] "ahmed - Feminist Killjoys (1).pdf"
## [102] "ahmed - Feminist Killjoys.pdf"
## [103] "all_loci-1.vcf"
## [104] "all_loci.vcf"
## [105] "allomtery_3_scatterplot3d (1).Rmd"
## [106] "Alone.pdf"
## [107] "amino acid chart.jpg"
## [108] "Analysis Essay_ Industrial Corn.pdf"
## [109] "Angela Zhu-11.9&11.11-Asynch-Response.docx"
## [110] "Angela--Textual Exploration.docx"
## [111] "Angela-Essay-2-GRADE-RUBRIC.doc"
## [112] "Angela-The City and Campus presentation.pdf"
## [113] "angelaLab4.py"
## [114] "angelayaya0815@gmail.com.pdf"
## [115] "Anh-Essay_2_final_draft.docx"
## [116] "Annotated bibliography.pdf"
## [117] "annotated-CRAPTest-Davis.pdf"
## [118] "Annotation.pdf"
## [119] "answerstohomework3summer2013.docx"
## [120] "AP 2012 #2 answer.PDF"
## [121] "AP CALC BC TEST.pdf"
## [122] "AP Calc BC timeline March 16 to April 3.docx"
## [123] "AP Calc Q1 (1).pdf"
## [124] "AP Calc Q1 (2).pdf"
## [125] "AP Calc Q1.pdf"
## [126] "AP Calc Q2 (1).pdf"
## [127] "AP Calc Q2.pdf"
## [128] "AP Course(2020).pdf"
## [129] "AP EXAM REVIEW Ch 1 - 2 WORKSHEET (1).pdf"
## [130] "AP EXAM REVIEW Ch 1 - 2 WORKSHEET (2).pdf"
## [131] "AP EXAM REVIEW Ch 1 - 2 WORKSHEET KEY (1).pdf"
## [132] "AP EXAM REVIEW Ch 1 - 2 WORKSHEET KEY.pdf"
## [133] "AP EXAM REVIEW Ch 1 - 2 WORKSHEET.pdf"
## [134] "AP EXAM REVIEW Ch 3 - 4 WORKSHEET (1).pdf"
## [135] "AP EXAM REVIEW Ch 3 - 4 WORKSHEET KEY (1).pdf"
## [136] "AP EXAM REVIEW Ch 3 - 4 WORKSHEET KEY.pdf"
## [137] "AP EXAM REVIEW Ch 3 - 4 WORKSHEET.pdf"
## [138] "AP EXAM REVIEW Ch 5 WORKSHEET (1).pdf"
## [139] "AP EXAM REVIEW Ch 5 WORKSHEET (2).pdf"
## [140] "AP EXAM REVIEW Ch 5 WORKSHEET.pdf"
## [141] "AP EXAM REVIEW Ch 6 WORKSHEET (1).pdf"
## [142] "AP EXAM REVIEW Ch 6 WORKSHEET KEY.pdf"
## [143] "AP EXAM REVIEW Ch 6 WORKSHEET.pdf"
## [144] "AP EXAM REVIEW Ch 7 WORKSHEET (1).pdf"
## [145] "AP EXAM REVIEW Ch 7 WORKSHEET KEY (1).pdf"
## [146] "AP EXAM REVIEW Ch 7 WORKSHEET KEY.pdf"
## [147] "AP EXAM REVIEW Ch 7 WORKSHEET.pdf"
## [148] "AP EXAM REVIEW Ch 8 WORKSHEET KEY.pdf"
## [149] "AP EXAM REVIEW Ch 8 WORKSHEET.pdf"
## [150] "AP EXAM REVIEW Ch 9 WORKSHEET KEY.pdf"
## [151] "AP EXAM REVIEW Ch 9 WORKSHEET.pdf"
## [152] "AP Physics.pdf"
## [153] "AP probs Ch 3 solns (1).pdf"
## [154] "AP probs Ch 3 solns.pdf"
## [155] "AP Stat (r^2).pdf"
## [156] "AP Stat 3.pdf"
## [157] "AP Stat 6.1.ppt"
## [158] "AP Stat Ch. 7.ppt"
## [159] "AP Stat.pdf"
## [160] "AP Statistics AP Exam Review Ch. 4 - 5.pptx"
## [161] "AP Stats Question 1.pdf"
## [162] "AP Stats Question 2.pdf"
## [163] "AP.pdf"
## [164] "ApE_OSX_modern_current.dmg"
## [165] "APS Ch 11 Lesson 1 Chi-Square Goodness-of-Fits Tests DAY 3 WORKSHEET (1).pdf"
## [166] "APS Ch 11 Lesson 1 Chi-Square Goodness-of-Fits Tests DAY 3 WORKSHEET.pdf"
## [167] "APS Ch 11 Lesson 2 Inference for Relationships DAY 3 WORKSHEET.pdf"
## [168] "Assignment1.java"
## [169] "Assignment3.java"
## [170] "atom-mac (1).zip"
## [171] "atom-mac.zip"
## [172] "Atom.app"
## [173] "audacity-macos-2.4.2.dmg"
## [174] "audacity-macosx-ub-2.1.1-screen-reader.dmg"
## [175] "audacity-manual-2.4.2.zip"
## [176] "B8A9AFDD-F7CE-46B0-BFBB-9B23290BB15A.heic"
## [177] "Bago-10.5-Asynch-Response.docx"
## [178] "baldwin-white-other-lies.pdf"
## [179] "Basic musical vocabulary_ Week 12 Rap 1.pdf"
## [180] "Basic musical vocabulary_ Week 13 Rap 2.pdf"
## [181] "Beat for Instrument Making (Rock Up-Beat) (1).mp3"
## [182] "Beat for Instrument Making (Rock Up-Beat)_data"
## [183] "Beat for Instrument Making (Rock Up-Beat).aup"
## [184] "Beat for Instrument Making (Rock Up-Beat).mp3"
## [185] "BeyondLabzConnect.dmg"
## [186] "Bio Exam 1 Rework (1).pdf"
## [187] "Bio Exam 1 Rework.pdf"
## [188] "BIO2HW7.pdf"
## [189] "BioLab Flow Chat.png"
## [190] "BioLab Purification1.jpg"
## [191] "BioLabDirectIsolation3.heic"
## [192] "BioLabPurification2.jpg"
## [193] "BioLabPurification3.jpg"
## [194] "Biopsychology and the Brain - part 2 (1).pptx"
## [195] "Biopsychology and the Brain - part 2.pptx"
## [196] "Biopsychology and the Brain (1).pptx"
## [197] "Biopsychology and the Brain.pptx"
## [198] "BIOSC 0058 Fall 2021 Syllabus .docx"
## [199] "Biosc 0068 Worksheet for reviewing other posters Sp 22.docx"
## [200] "bird_snps_remove_NAs.html"
## [201] "bird_snps_remove_NAs.Rmd"
## [202] "Boiling Point Elevation (1).pdf"
## [203] "Boiling Point Elevation (2).pdf"
## [204] "Boiling Point Elevation (3).pdf"
## [205] "Boiling Point Elevation.pdf"
## [206] "book.jpg"
## [207] "Borong Tsai Unit 1 Project.mp3"
## [208] "Brainstorm (1) (1).pdf"
## [209] "Brainstorm (1) (2).pdf"
## [210] "Brainstorm (1).pdf"
## [211] "Brainstorm.pdf"
## [212] "BU.pdf"
## [213] "Bury beetles biology.docx"
## [214] "BUS 100 CRN 93588 Syllabus (1).pdf"
## [215] "BUS 100 CRN 93588 Syllabus.pdf"
## [216] "BUS 100.numbers"
## [217] "Calc1_Trofimov_Xiaoyu_Quiz2_20200924 2.pdf"
## [218] "Calc1_Trofimov_Xiaoyu_Quiz2_20200924.pdf"
## [219] "Calc1LabNote_Trofimov_03_20200908 (1).pdf"
## [220] "Calc1LabNote_Trofimov_03_20200908.pdf"
## [221] "Calculate grade as of 4.19.21.docx"
## [222] "calendar.ics"
## [223] "CAPITULO PRELIMINAR, MOSAICOS.docx"
## [224] "Case Competition Learning Agreement - 2022 (1).docx"
## [225] "Case Competition Learning Agreement - 2022 (1).pdf"
## [226] "Case Competition Learning Agreement - 2022.pdf"
## [227] "Catharine-A.-MacKinnon-Andrea-Dworkin-Pornography-and-Civil-Rights zh.pdf"
## [228] "cells-11-01048.pdf"
## [229] "center_function (1).R"
## [230] "center_function.R"
## [231] "CER.pdf"
## [232] "CERAMICS VOCABULARY.doc"
## [233] "Certificate_21679734 (1).pdf"
## [234] "Certificate_21679734.pdf"
## [235] "CH_7_and_8_Review_Sheet_solns (1).pdf"
## [236] "CH_7_and_8_Review_Sheet_solns (2).pdf"
## [237] "CH_7_and_8_Review_Sheet_solns.pdf"
## [238] "Ch. 11 Review WS answers.pdf"
## [239] "Ch.8 TRIPLE ENTRY JOURNAL .pdf"
## [240] "ch06.doc"
## [241] "Ch3 TRIPLE ENTRY JOURNAL.pdf"
## [242] "ChangingMotion.doc"
## [243] "Chapter 19 Problem Set.pdf"
## [244] "chapter_19_text.docx"
## [245] "Chapter_7_Outline_-_Key.pdf"
## [246] "Chapter-13_Lecture-Slides.pdf"
## [247] "Chapter-13-Problems (hints).pdf"
## [248] "Chapter-15_Lecture-Slides.pdf"
## [249] "Chapter-18_Lecture-Slides.pdf"
## [250] "Chapter-19_Lecture-Slides.pdf"
## [251] "Chapter-20_Lecture-Slides.pdf"
## [252] "Chapter-21_Lecture-Slides.pdf"
## [253] "Chapter-22_Lecture-Slides.pdf"
## [254] "Chapter-23_Lecture-Slides.pdf"
## [255] "Chapter-24_Lecture-Slides.pdf"
## [256] "Chapter-25_Lecture-Slides.pdf"
## [257] "Chem1 Lab Report 1.pdf"
## [258] "Chem1 Quiz7 Part2.pdf"
## [259] "Chem220 Schedule Su21 v2.pdf"
## [260] "CIS 117 Coding Standard .pdf"
## [261] "CLARK - PHYS 0212-0219 - Lecture 10 - Reflection and Refraction.pdf"
## [262] "Class participation_ basic musical vocabulary.pdf"
## [263] "Class participation_ introduction to podcasting.pdf"
## [264] "Class participation_ song form.pdf"
## [265] "cluster_analysis_portfolio.Rmd"
## [266] "CM-1.mp3"
## [267] "CM-2.mp3"
## [268] "CM-3.mp3"
## [269] "code_checkpoint_vcfR.Rmd"
## [270] "CODE_CHECKPOINT-first_rstudio_script.R"
## [271] "combinepdf (1).pdf"
## [272] "combinepdf (2).pdf"
## [273] "combinepdf.pdf"
## [274] "Consciousness and Attention (1).pptx"
## [275] "Consciousness and Attention (2).pptx"
## [276] "Consciousness and Attention.pptx"
## [277] "Consider the Lobster .pdf"
## [278] "Consider the Lobster Summary (1).docx"
## [279] "Consider the Lobster summary (1).pdf"
## [280] "Consider the Lobster Summary (2).docx"
## [281] "Consider the Lobster Summary.docx"
## [282] "Consider the Lobster summary.pdf"
## [283] "Copy of Zhang Huan.pptx"
## [284] "Corn_Essay.pdf"
## [285] "Course Syllabus-1 (1).pdf"
## [286] "Course Syllabus-1.pdf"
## [287] "Course Syllabus-2.pdf"
## [288] "Course Syllabus-4.pdf"
## [289] "CRAAP_test_with_rubric (1).docx"
## [290] "CRAAP_test_with_rubric (2).docx"
## [291] "CRAAP_test_with_rubric.docx"
## [292] "CRAAP_test_with_rubric.pdf"
## [293] "CRAPTest-Christopher_Campos.pdf"
## [294] "Crenshaw Demarginalizing the Intersections (1).pdf"
## [295] "Crenshaw Demarginalizing the Intersections.pdf"
## [296] "Critical Interpretation (1).docx"
## [297] "Critical Interpretation Revision.docx"
## [298] "Critical Interpretation.docx"
## [299] "Critique Essay Erin Adams FT.docx"
## [300] "Critique Peer Review.docx"
## [301] "CSM Chem2 Exam3 Written (1).pdf"
## [302] "CSM Chem2 Exam3 Written (2).pdf"
## [303] "CSM Chem2 Exam3 Written.pdf"
## [304] "CSM PHY210 Exam2.pdf"
## [305] "CSM Phys 210 Exam 3, 50%.....pdf"
## [306] "CSSProfile-EAABKL3.pdf"
## [307] "CulturalProject_SPAN101_Fall 2020.docx"
## [308] "d5a7_2019618171016_NeteaseMusic_2.1.1_790_web.dmg"
## [309] "Danny Boy (spoken) (1).mp3"
## [310] "Danny Boy (spoken).mp3"
## [311] "Danny Boy (sung) (1).mp3"
## [312] "Danny Boy (sung).mp3"
## [313] "de_Beauvoir_The_Second_Sex.pdf"
## [314] "DeepL.dmg"
## [315] "demo_message.py"
## [316] "Diet Reflection Essay (1).docx"
## [317] "Diet Reflection Essay.docx"
## [318] "Diet Reflection Essay.odt"
## [319] "django-master"
## [320] "django-master.tar.gz"
## [321] "Douglas-Essay_2.pdf"
## [322] "DS_Store"
## [323] "DSGD_63_Ex_02_A1_Template_grid.tmp"
## [324] "duchnowski-10.21-asynch-response-2 (1).docx"
## [325] "duchnowski-10.21-asynch-response-2.docx"
## [326] "duchnowski-10.26-asynch-response.docx"
## [327] "Duchnowski-11.04-Asynchronous Response.docx"
## [328] "duchnowski-october.19-asynch-response.docx"
## [329] "E-mail What Not to Write.pdf"
## [330] "e1(0220)_2020_fall_sample_sln.pdf"
## [331] "e2(0220)_2020_fall_sample_sln.pdf"
## [332] "EC #2- Exam 1 Wrapper.pdf"
## [333] "Eclipse.app"
## [334] "eco-ur-fascism.pdf"
## [335] "Econ100 L3 Allocative Efficiency.pdf"
## [336] "Econ100 Week2b PPF.pdf"
## [337] "End of term Letter.docx"
## [338] "energy-skate-park_en (1).jar"
## [339] "energy-skate-park_en (2).jar"
## [340] "energy-skate-park_en.jar"
## [341] "ENG100--CRAAP (1).pdf"
## [342] "ENG100--CRAAP.pdf"
## [343] "ENG100--WHAT MOTIVATES YOUR ARGUMENT (1).pdf"
## [344] "ENG100--WHAT MOTIVATES YOUR ARGUMENT (2).pdf"
## [345] "ENG100--WHAT MOTIVATES YOUR ARGUMENT.pdf"
## [346] "ENG100-ONH-SYLLABUS (1).doc"
## [347] "ENG100-ONH-SYLLABUS (2).doc"
## [348] "ENG100-ONH-SYLLABUS (3).doc"
## [349] "ENG100-ONH-SYLLABUS (4).doc"
## [350] "ENG100-ONH-SYLLABUS (5).doc"
## [351] "ENG100-ONH-SYLLABUS.doc"
## [352] "ENGCMP 0200-Lecture Notes.pdf"
## [353] "ENGL 100 Reading and Writing Autobiography.pdf"
## [354] "ENGL100--FINDING CREDIBLE and RELEVANT INFORMATION ON THE WEB.pdf"
## [355] "Essay #2. Compile a Works Cited.docx"
## [356] "Essay 1 Rough Draft.pdf"
## [357] "Essay 1_ Summary & Response.pdf"
## [358] "Essay 1_Summary and Response (1).doc"
## [359] "Essay 1_Summary and Response.doc"
## [360] "Essay 2 outline.docx"
## [361] "Essay 2 outline.pdf"
## [362] "essay 2 peer review (1).docx"
## [363] "essay 2 peer review.docx"
## [364] "ESSAY 2 PEER REVIEW.pdf"
## [365] "Essay 2 Rough Draft.pdf"
## [366] "Essay 2_Rhetorical Analysis (1).doc"
## [367] "Essay 2_Rhetorical Analysis.doc"
## [368] "Essay 3 (1).pdf"
## [369] "Essay 3.pdf"
## [370] "Essay 3+4 Final Draft (1).pdf"
## [371] "Essay 3+4 Final Draft (2).pdf"
## [372] "Essay 3+4 Final Draft (3).pdf"
## [373] "Essay 3+4 Final Draft.pdf"
## [374] "Essay 4 draft (1).docx"
## [375] "Essay 4 draft.docx"
## [376] "Essay 4 outline (1).pdf"
## [377] "Essay 4 outline.pdf"
## [378] "ESSAY 4 PEER REVIEW.pdf"
## [379] "Essay Outline - Rebeka Griswold-1.pdf"
## [380] "Essay_3_4_Final_Draft_3_.pdf"
## [381] "Essay_3_Structure (1).doc"
## [382] "Essay_3_Structure (2).doc"
## [383] "Essay_3_Structure.doc"
## [384] "Essay_3+4_prompt.docx"
## [385] "Essay_4_Structure-1.pdf"
## [386] "Essay_4_Structure.pdf"
## [387] "ESSAY-1-PEER-REVIEW.doc"
## [388] "ESSAY-2-PEER-REVIEW.doc"
## [389] "ESSAY-2-PEER-REVIEW.pages"
## [390] "ESSAY-4-PEER-REVIEW (1).doc"
## [391] "ESSAY-4-PEER-REVIEW.doc"
## [392] "Ethical and socially responsible(2).m4a"
## [393] "eWrite_Consent_Version_0.04.pdf"
## [394] "Ex1_Span 0101_Fall 2020_aprobado (1).docx"
## [395] "Ex1_Span 0101_Fall 2020_aprobado.docx"
## [396] "Exam 1 Practice - Key (1).pdf"
## [397] "Exam 1 Practice - Key.pdf"
## [398] "Exam 3 Practice.pdf"
## [399] "Exam 3 review questions.docx"
## [400] "Exam Wrapper.docx"
## [401] "Exam Wrapper.docx.pdf"
## [402] "Experiment 2 - What Does It Even Mean_.docx"
## [403] "Experiment 3 - Unearthing Other Writers' Source Material.docx"
## [404] "Experiment 8_ One Revised Section.docx"
## [405] "Exposome_WORKSHEET (1).pdf"
## [406] "Exposome_WORKSHEET.pdf"
## [407] "F7B50EF3-7C2A-4818-9237-774018230D9B.jpg"
## [408] "feature_engineering_intro_2_functions-part2.Rmd"
## [409] "feature_engineering.Rmd"
## [410] "Film Report from 1940 and 2010 Confucius.pdf"
## [411] "Final Draft Rhetorical Analysis.pdf"
## [412] "Final S21.docx"
## [413] "Final_Draft_Rhetorical_Analysis.pdf"
## [414] "Final_Review_Slides.pdf"
## [415] "Final_SPAN0101_Fall 2020_Angela Zhu (1).pages"
## [416] "Final_SPAN0101_Fall 2020_Angela Zhu.pages"
## [417] "Final_SPAN0101_Fall 2020_your name-1.docx"
## [418] "Finding_credible_and_relevant_sources.pdf"
## [419] "Firefox 79.0.dmg"
## [420] "First work experience (Angela Zhu) (1).docx"
## [421] "First work experience (Angela Zhu).docx"
## [422] "First work experience (Angela Zhu).pdf"
## [423] "Flicker List_Setup_2.4.0.dmg"
## [424] "Fliqlo 1.8.2 (1).dmg"
## [425] "Fliqlo 1.8.2.dmg"
## [426] "FOB_04_Transcription.pptx"
## [427] "FoB_Fall21.pdf"
## [428] "Fool's Garden - Lemon Tree.mp3"
## [429] "Foster-9_2_20-asynch-response.docx"
## [430] "FP Week 1-Memoir Project.pdf"
## [431] "FRQ Quiz Diff Eq..pdf"
## [432] "fst_exploration_in_class-STUDENT.Rmd"
## [433] "Fuentes-10.12-Asynch-Response.pdf"
## [434] "Fuentes-10.28-Asynch-Response.pdf"
## [435] "Full Plate Titer.jpeg"
## [436] "Gaard - Ecofeminism zh.pdf"
## [437] "Gender Anna Yansuhkevich (1).pdf"
## [438] "Gender Anna Yansuhkevich.pdf"
## [439] "gettingStartedwDjango (1).pdf"
## [440] "gettingStartedwDjango.pdf"
## [441] "gmail头像.jpg"
## [442] "Gmaps deep time.xlsx"
## [443] "googlechrome (1).dmg"
## [444] "googlechrome.dmg"
## [445] "Gov。。.mp4"
## [446] "Grade calculator v2 (1).xlsx"
## [447] "Grade calculator v2.xlsx"
## [448] "GSWS 500_1135.pdf"
## [449] "GSWS First Day Info Sheet (1).pdf"
## [450] "GSWS First Day Info Sheet.docx"
## [451] "GSWS First Day Info Sheet.pdf"
## [452] "GSWS_Yue Suo_Paper 1 (1).pdf"
## [453] "GSWS_Yue Suo_Paper 1.pdf"
## [454] "GSWS0500-6th Reading Response.pdf"
## [455] "GSWS0500-Feminist Critique Essay Draft.docx.pdf"
## [456] "GSWS0500-Proposal Final Essay.docx (1).pdf"
## [457] "GSWS0500-Proposal Final Essay.docx.pdf"
## [458] "Hatfull 2020 (1).pdf"
## [459] "Hatfull 2020 (2).pdf"
## [460] "Hatfull 2020.pdf"
## [461] "High-School-Student.xlsx"
## [462] "How Should We Eat_.docx"
## [463] "HowtoWriteyourUCActivitiesList.pdf"
## [464] "HW14 data.xlsx"
## [465] "Ikson - Alive (Official).mp3"
## [466] "image1.jpeg"
## [467] "IMG_0585.MOV"
## [468] "IMG_0678.JPG"
## [469] "IMG_0788.PNG"
## [470] "IMG_0882 2.HEIC"
## [471] "IMG_0882.HEIC"
## [472] "IMG_0883 2.HEIC"
## [473] "IMG_0883.HEIC"
## [474] "IMG_0884 2.HEIC"
## [475] "IMG_0884.HEIC"
## [476] "IMG_0885 2.HEIC"
## [477] "IMG_0885.HEIC"
## [478] "IMG_0886 2.HEIC"
## [479] "IMG_0886.HEIC"
## [480] "IMG_0887 2.HEIC"
## [481] "IMG_0887.HEIC"
## [482] "IMG_0888 2.HEIC"
## [483] "IMG_0888.HEIC"
## [484] "IMG_0889 2.HEIC"
## [485] "IMG_0889.HEIC"
## [486] "IMG_0890 2.HEIC"
## [487] "IMG_0890.HEIC"
## [488] "IMG_0891 2.HEIC"
## [489] "IMG_0891.HEIC"
## [490] "IMG_0892 2.HEIC"
## [491] "IMG_0892.HEIC"
## [492] "IMG_0893 2.HEIC"
## [493] "IMG_0893.HEIC"
## [494] "IMG_0914.JPG"
## [495] "IMG_0982.PNG"
## [496] "IMG_1004.heic"
## [497] "IMG_1005.heic"
## [498] "IMG_1063.jpg"
## [499] "IMG_1064.jpg"
## [500] "IMG_1199.heic"
## [501] "IMG_1227.jpg"
## [502] "IMG_1238.jpg"
## [503] "IMG_1244.jpg"
## [504] "IMG_1248.JPG"
## [505] "IMG_1461 2.HEIC"
## [506] "IMG_2721.HEIC"
## [507] "IMG_2721.jpg"
## [508] "IMG_2722.HEIC"
## [509] "IMG_2722.jpg"
## [510] "IMG_2758.HEIC"
## [511] "IMG_2759.HEIC"
## [512] "IMG_2760.HEIC"
## [513] "IMG_2761.HEIC"
## [514] "IMG_2762.HEIC"
## [515] "IMG_2763.HEIC"
## [516] "IMG_2764.jpg"
## [517] "IMG_2765.jpg"
## [518] "IMG_2766.HEIC"
## [519] "IMG_2767.HEIC"
## [520] "IMG_2768.HEIC"
## [521] "IMG_2769.HEIC"
## [522] "IMG_3131 copy.JPG"
## [523] "IMG_3131.JPG"
## [524] "IMG_3132 copy.JPG"
## [525] "IMG_3132.JPG"
## [526] "IMG_3133 copy.JPG"
## [527] "IMG_3133.JPG"
## [528] "IMG_3134 copy.JPG"
## [529] "IMG_3134.JPG"
## [530] "IMG_3135 copy.JPG"
## [531] "IMG_3135.JPG"
## [532] "IMG_3136 copy.JPG"
## [533] "IMG_3136.JPG"
## [534] "IMG_3137 copy.JPG"
## [535] "IMG_3137.JPG"
## [536] "IMG_3138 copy.JPG"
## [537] "IMG_3138.JPG"
## [538] "IMG_3139 copy.JPG"
## [539] "IMG_3139.JPG"
## [540] "IMG_3140 copy.JPG"
## [541] "IMG_3140.JPG"
## [542] "IMG_3681.HEIC"
## [543] "IMG_3682.HEIC"
## [544] "IMG_3735.HEIC"
## [545] "IMG_3736.HEIC"
## [546] "IMG_4386.JPG"
## [547] "IMG_4477.HEIC"
## [548] "IMG_4478.HEIC"
## [549] "IMG_4479.HEIC"
## [550] "IMG_4480.HEIC"
## [551] "IMG_4481.HEIC"
## [552] "IMG_4482.HEIC"
## [553] "IMG_4559.JPG"
## [554] "IMG_7084.heic"
## [555] "IMG_7185.MOV"
## [556] "Industrial Analysis Essay Summer 2020.docx"
## [557] "Industrial Corn Outline (1).docx"
## [558] "Industrial Corn Outline.docx"
## [559] "Industrial Corn Outline.pdf"
## [560] "Industrial_ Corn Outline (1).pdf"
## [561] "Industrial_ Corn Outline.pdf"
## [562] "Information Literacy Tutorial - Annotated Bibliography.docx"
## [563] "Information Literacy Tutorial - Annotated Bibliography.pdf"
## [564] "Information_Literacy_-_Annotated_Bibliography__final__1___3_.docx"
## [565] "Information_Literacy_-_Annotated_Bibliography__final__1___3_.pages"
## [566] "Integrating quotes.pdf"
## [567] "Into the Wild Essay Final.pdf"
## [568] "Intro to Psy Exam3.pdf"
## [569] "Intro to Psych Exam2 Notes.docx"
## [570] "Intro to Psych Exam3 Notes.docx"
## [571] "Intro to Psych Exam3 Notes.pages"
## [572] "Intro.m4a"
## [573] "IntroBioQuestionsandanswerarchive (1).pdf"
## [574] "IntroBioQuestionsandanswerarchive.pdf"
## [575] "Introduction to Psychology slides.pptx"
## [576] "ips10e_excel_data_sets (1).zip"
## [577] "ips10e_excel_data_sets.zip"
## [578] "Isolation#5.HEIC"
## [579] "Jack Ma BUS100.jpg"
## [580] "Jack Ma BUS100.mp4"
## [581] "Jacobs-Sera et al 2012 Figure Facts Worksheet.docx"
## [582] "jdk-18_macos-x64_bin.dmg"
## [583] "Joey G OD ESSAY OUTLINE.pdf"
## [584] "jre-8u341-macosx-x64.dmg"
## [585] "Juntao_Huang_Industrial Corn Outline Peer Review.pdf"
## [586] "Keana Malolot Diet Reflection Draft (1).docx"
## [587] "Keana Malolot Diet Reflection Draft.docx"
## [588] "Koyama transfeministmanifesto.pdf"
## [589] "Kramer-10.26-asynch-response-1.pdf"
## [590] "LA Times article.docx"
## [591] "Lab 01 Report - Changing Motion (1).pdf"
## [592] "Lab 01 Report - Changing Motion (10).pdf"
## [593] "Lab 01 Report - Changing Motion (11).pdf"
## [594] "Lab 01 Report - Changing Motion (2).pdf"
## [595] "Lab 01 Report - Changing Motion (3).pdf"
## [596] "Lab 01 Report - Changing Motion (4).pdf"
## [597] "Lab 01 Report - Changing Motion (5).pdf"
## [598] "Lab 01 Report - Changing Motion (6).pdf"
## [599] "Lab 01 Report - Changing Motion (7).pdf"
## [600] "Lab 01 Report - Changing Motion (8).pdf"
## [601] "Lab 01 Report - Changing Motion (9).pdf"
## [602] "Lab 01 Report - Changing Motion.docx"
## [603] "Lab 01 Report - Changing Motion.pdf"
## [604] "Lab 02 Report - Force and Motion.docx"
## [605] "Lab 03 Report - Combining Forces.docx"
## [606] "Lab 04 Report - Newtons Third Law and Conservation of Momentum (1).docx"
## [607] "Lab 04 Report - Newtons Third Law and Conservation of Momentum.docx"
## [608] "Lab 06 Report - Conservation of Energy.docx"
## [609] "Lab 08 Report - Introduction to Capacitors and RC Circuits.docx"
## [610] "Lab 09 Report - Magnetism and Electromagnetism.docx"
## [611] "Lab Meeting1 Slides-ZL&AZ.pptx"
## [612] "Lab Report Format .docx"
## [613] "Lab-10.txt"
## [614] "Lab1 (3).java"
## [615] "Lab1 (4).java"
## [616] "Lab2 (1).java"
## [617] "Lab2.java"
## [618] "Lab3.java"
## [619] "Lab4.java"
## [620] "Lab5 (1).java"
## [621] "Lab5 (2).java"
## [622] "Lab5.java"
## [623] "Lab6.java"
## [624] "Lab6b.java"
## [625] "Lab6Run.jpeg"
## [626] "Lab7Instructions.java"
## [627] "Lab8.java"
## [628] "Lab9Output.png"
## [629] "Learning (1).pptx"
## [630] "Learning.pptx"
## [631] "Lec8solutions (1).pdf"
## [632] "Lec8solutions.pdf"
## [633] "Lecture (1).ppt"
## [634] "lecture-introd2RStudio-with_scripts.pdf"
## [635] "Lecture.ppt"
## [636] "Library_research_handout.pdf"
## [637] "lobsterarticle(1) (1).pdf"
## [638] "lobsterarticle(1).pdf"
## [639] "lovely-hand-drawn-feminism-compositionq.zip"
## [640] "LR Acid Base Classification of Salts.pdf"
## [641] "LR An Unknown Solid Weak Acid.pdf"
## [642] "LR Analysis of a Ferrous Chloride Sample.pdf"
## [643] "LR Qualitative Analysis of Cations.pdf"
## [644] "LR titration of weak acid.pdf"
## [645] "LR Titration_ Unknown HCl.pdf"
## [646] "LR_ The Balance Between Enthalpy and Entropy.pdf"
## [647] "MacKeeper.5.6.11.pkg"
## [648] "Make Optimum Webbed Plate (1).jpeg"
## [649] "Make Optimum Webbed Plate (2).jpeg"
## [650] "Make Optimum Webbed Plate.jpeg"
## [651] "MATH1431W03Test4Ans.doc"
## [652] "McGraw-Hill's SAT Subject Test Math-2.pdf"
## [653] "Memory (1).pptx"
## [654] "Memory (2).pptx"
## [655] "Memory.pptx"
## [656] "Meningitis 2020-2021 (1).pdf"
## [657] "Meningitis 2020-2021.pdf"
## [658] "Metaphysics--Angela (1).pdf"
## [659] "Metaphysics--Angela.pdf"
## [660] "mgtv-client-6.1.7-mango (1).dmg"
## [661] "mgtv-client-6.1.7-mango.dmg"
## [662] "mgtv-client-6.1.7-mango2.dmg"
## [663] "Miller_12DaysOfStatistics.doc"
## [664] "minitab_FY22 (1).zip"
## [665] "minitab_FY22.zip"
## [666] "Minitab.v19.2020.2.0 (1).zip"
## [667] "Minitab.v19.2020.2.0 (2).zip"
## [668] "Minitab.v19.2020.2.0.zip"
## [669] "MLA Format (1).pdf"
## [670] "MLA Format.pdf"
## [671] "MLF Report.pdf"
## [672] "Mohanty_Under Western Eyes-1.pdf"
## [673] "morrison-playing-in-the-dark (1).pdf"
## [674] "morrison-playing-in-the-dark.pdf"
## [675] "MUSIC 0121 Week1-Vocab.docx (1).pdf"
## [676] "MUSIC 0121 Week1-Vocab.docx.pdf"
## [677] "MUSIC0121 Week2_data"
## [678] "MUSIC0121 Week2.aup"
## [679] "Noun Phrase Appositive worksheet (1).doc"
## [680] "Noun Phrase Appositive worksheet.doc"
## [681] "NOUN PHRASE APPOSITIVES (NPAs).pdf"
## [682] "Observation notes for Bernie Sanders speech.pdf"
## [683] "Order 1547238637 Pop Culture Analysis_Outline.docx"
## [684] "Organic Chemistry Structure and Function by K. Peter C. Vollhardt Neil E Schore (z-lib.org).djvu"
## [685] "Out of the Text.docx"
## [686] "outline draft (1).docx"
## [687] "outline draft (2).docx"
## [688] "outline draft.docx"
## [689] "Outline-Black Matters.docx"
## [690] "Outline-Black Matters.pdf"
## [691] "Outline-form (1).pdf"
## [692] "Outline-form.pdf"
## [693] "PantleCULRVol35.pdf"
## [694] "pconline1559561959904_52000039575613174651.exe"
## [695] "PDF reading_W6 Thu_A Short History of Chinese Philosophy_Yinyang_Cosmogony.pdf"
## [696] "Personal Investigation (1).docx"
## [697] "Personal Investigation.docx"
## [698] "phage (1).fasta"
## [699] "phage (2).fasta"
## [700] "Phage Phingerprinting Gel Data Card.pptx"
## [701] "PHY210 Quiz 1 Intro.pdf"
## [702] "piano.mp3"
## [703] "podcast_Chi-1.mp3"
## [704] "Pop Culture Analysis Peer Review.docx"
## [705] "Pop Culture Analysis.docx.pdf"
## [706] "Pop Culture Essay Draft.pdf"
## [707] "portfolio_ggpubr_intro-2 (1).Rmd"
## [708] "portfolio_ggpubr_intro-2 (2).Rmd"
## [709] "portfolio_ggpubr_intro-2 (3).Rmd"
## [710] "portfolio_ggpubr_intro-2 (4).Rmd"
## [711] "portfolio_ggpubr_intro-2.Rmd"
## [712] "portfolio_ggpubr_log_transformation.Rmd"
## [713] "Potential Brochure.docx"
## [714] "pq8anumber4purecompmaxproftab (1).avi"
## [715] "pq8anumber4purecompmaxproftab.avi"
## [716] "Practice Test- Ch 10 and 11.pdf"
## [717] "Problems 5 Spring 2022 updated.pdf"
## [718] "PROOFREADING EXERCISE 1 (1).pdf"
## [719] "PROOFREADING EXERCISE 1.pdf"
## [720] "PROOFREADING EXERCISE.pdf"
## [721] "Proofreading_exercise (1).pdf"
## [722] "Proofreading_exercise.pdf"
## [723] "ProtocolStartUp-1-20-16-Copy.doc"
## [724] "Psych Final Notes(1).pages"
## [725] "Psych Notes.docx"
## [726] "Psychological Research (1).pptx"
## [727] "Psychological Research (2).pptx"
## [728] "Psychological Research.pptx"
## [729] "PUNCTUATION RULES FOR JOINING WORDS (1).pdf"
## [730] "PUNCTUATION RULES FOR JOINING WORDS.pdf"
## [731] "python-3.7.4-macosx10.9.pkg"
## [732] "Q27.png"
## [733] "q4.png"
## [734] "QQ_V6.5.3.dmg"
## [735] "QQ截图20200205154628.png"
## [736] "QQ截图20200205155031.png"
## [737] "question 1A.pdf"
## [738] "question 1B.pdf"
## [739] "question 1C.pdf"
## [740] "question 2.pdf"
## [741] "Quiz FRQ 1.pdf"
## [742] "RA draft (1).docx"
## [743] "RA draft.docx"
## [744] "Rachel_Research-essay.pdf"
## [745] "receipt_Essay 3+4 final Draft.pdf"
## [746] "Recitation 4 Spring 2022 key New.docx"
## [747] "removing_fixed_alleles.html"
## [748] "removing_fixed_alleles.Rmd"
## [749] "Report Form Kinetic Studies of Food Dyes (1).docx"
## [750] "Report Form Kinetic Studies of Food Dyes (1).docx.pdf"
## [751] "Report Form Kinetic Studies of Food Dyes.docx"
## [752] "Report Form Le Châteliers Principle.docx"
## [753] "Report Form Le Châteliers Principle.docx.pdf"
## [754] "Report.docx"
## [755] "ResponseSummary.pdf"
## [756] "Revised Rhetorical Analysis.pdf"
## [757] "Rhetorical-Analysis-Outline-template.pdf"
## [758] "Rhetorical-analysis-review.pdf"
## [759] "Rich_Compulsory-heterosexuality-and-lesbian-existence (1).pdf"
## [760] "Rich_Compulsory-heterosexuality-and-lesbian-existence (2).pdf"
## [761] "Rich_Compulsory-heterosexuality-and-lesbian-existence.pdf"
## [762] "rsconnect"
## [763] "RStudio-2022.07.1-554.dmg"
## [764] "rtools42-5355-5357.exe"
## [765] "S03 - North.pdf"
## [766] "Salamon - Boys of the Lex.pdf"
## [767] "Sample Papers (Rubin).docx"
## [768] "Sample questions with answers-2.pdf"
## [769] "Sample questions with answers.docx"
## [770] "Sample questions without answers (1).docx"
## [771] "Sample questions without answers (2).docx"
## [772] "Sample questions without answers-1.pdf"
## [773] "Sample questions without answers.docx"
## [774] "sat2 math new og-3.pdf"
## [775] "SATStudentScoreReport_1571870736723.pdf"
## [776] "saunders-braindead.pdf"
## [777] "Scan888.pdf"
## [778] "Scigliano-09.10-Asynch-Projects (1).docx"
## [779] "Scigliano-09.10-Asynch-Projects.docx"
## [780] "Scigliano-09.14-Asynch-Response (1).docx"
## [781] "Scigliano-09.14-Asynch-Response.docx"
## [782] "Scigliano-09.16-Asynch-Response.docx"
## [783] "Scigliano-09.21-Asynch-Response.docx"
## [784] "Scigliano-09.23-Asynch-Project.docx"
## [785] "Scigliano-10.05-Asynch Response.docx"
## [786] "Scigliano-10.12-Asynch-Response.docx"
## [787] "Scigliano-10.19-Asynch-Response.docx"
## [788] "Scigliano-10.21-Asynch-Project.docx"
## [789] "SCIGRESS_V3.3.3.dmg"
## [790] "SCIGRESS_V3.4.3.dmg"
## [791] "Screen Recording 2019-10-20 at 3.06.28 PM.jpg"
## [792] "Screen Shot 2020-08-21 at 12.56.58 AM.png"
## [793] "Screen Shot 2021-02-16 at 5.03.28 PM.png"
## [794] "Screen Shot 2022-12-03 at 11.58.10 PM.png"
## [795] "SEAPHAGES Lab Poster-1.pptx"
## [796] "SEAPHAGES Results Poster (1).pdf"
## [797] "SEAPHAGES Results Poster (2).pdf"
## [798] "SEAPHAGES Results Poster (3).pdf"
## [799] "SEAPHAGES Results Poster.pdf"
## [800] "Section_7_1.ppt"
## [801] "Sensation and Perception.pptx"
## [802] "Sentence_types.pdf"
## [803] "Sentence-types-exercise.docx"
## [804] "Sep 30 2022 - FINAL - GLOBAL HEALTH CASE COMPETITION (1).pdf"
## [805] "Sep 30 2022 - FINAL - GLOBAL HEALTH CASE COMPETITION.pdf"
## [806] "Setting-up-Essay-4.docx"
## [807] "shellscriptingbasics.docx"
## [808] "shimo150.dmg"
## [809] "Ship2Pitt(2021).pdf"
## [810] "SHM Worksheet 2 (1).doc"
## [811] "SHM Worksheet 2.doc"
## [812] "simple_harmonic_motion_worksheet.docx"
## [813] "sogou_mac_guanwang_611 (1).zip"
## [814] "sogou_mac_guanwang_611.app"
## [815] "sogou_mac_guanwang_611.zip"
## [816] "SOLUTIONS.Chapters1-5.doc"
## [817] "SOLUTIONS.Chapters6-13.doc"
## [818] "Sound Video.mp4"
## [819] "sound walk.m4a"
## [820] "Sound_Worksheet_1-KEY.pdf"
## [821] "Soundflower-2.0b2 (1).dmg"
## [822] "Soundflower-2.0b2 (2).dmg"
## [823] "Soundflower-2.0b2.dmg"
## [824] "SP1_Assignment 1_Perfil Universitario (video).docx"
## [825] "Spanish Assignment 3.docx"
## [826] "Spanish Cultural Project.docx"
## [827] "Spanish Quiz #1.docx"
## [828] "Spot titer.png"
## [829] "SpotifyInstaller.zip"
## [830] "SpotifySetup.exe"
## [831] "Stat 1000 take home exam (1).pdf"
## [832] "Stat 1000 take home exam.pdf"
## [833] "Stat1000 ch1 HW - 10e.docx"
## [834] "Stat1000 ch3 HW - 10e.docx"
## [835] "Stat1000 ch8 HW - 10e.docx"
## [836] "Stat1000 ch9 HW - 10e.docx"
## [837] "Stat1000 HW8 (1).pdf"
## [838] "Stat1000 HW8.pdf"
## [839] "Stat1000_Final_Part1 (1).pdf"
## [840] "Stat1000_Final_Part1.pdf"
## [841] "Stat1000HW10.docx"
## [842] "Stat1000HW2 (1).docx"
## [843] "Stat1000HW2 (2).docx"
## [844] "Stat1000HW2 (3).docx"
## [845] "Stat1000HW2 (4).docx"
## [846] "Stat1000HW2 (5).docx"
## [847] "Stat1000HW2 (6).docx"
## [848] "Stat1000HW2 (7).docx"
## [849] "Stat1000HW2 (8).docx"
## [850] "Stat1000HW2 (9).docx"
## [851] "Stat1000HW2.docx"
## [852] "Stat1000HW3 Q5a.jpg"
## [853] "steam (1).dmg"
## [854] "steam.dmg"
## [855] "StemCellDataNugget.pdf"
## [856] "Study guide 3.pdf"
## [857] "SU(first page).pdf"
## [858] "SU(second page).pdf"
## [859] "Summary _Consider the Lobster - Rebeka Griswold (1).pdf"
## [860] "Summary _Consider the Lobster - Rebeka Griswold.pdf"
## [861] "Summary (1).pdf"
## [862] "Summary_of_Consider_the_Lobster.docx"
## [863] "Summary.pdf"
## [864] "SUPER JUNIOR ( 슈퍼주니어) 'Lo Siento (Feat. Leslie Grace)' [Color Coded Lyrics] HanRomEng.mp3"
## [865] "Super Junior (슈퍼주니어) BONAMANA (미인아) (Color Coded Lyrics) [HanRomEng].mp3"
## [866] "Super Junior (슈퍼주니어) No Other (너 같은 사람 또 없어) (Color Coded Lyrics) [HanRomEng].mp3"
## [867] "Super Junior (슈퍼주니어) SORRY, SORRY (Color Coded Lyrics) [HanRomEng].mp3"
## [868] "Syllabus CHEM 0110 Spring 21.docx"
## [869] "t_test_prop_test_examples_key.pdf"
## [870] "Taking-notes-for-rhetorical-analysis.doc"
## [871] "TEJ_guide_for_non-fiction (1).pdf"
## [872] "TEJ_guide_for_non-fiction (2).pdf"
## [873] "TEJ_guide_for_non-fiction (3).pdf"
## [874] "TEJ_guide_for_non-fiction (4).pdf"
## [875] "TEJ_guide_for_non-fiction.pdf"
## [876] "TEJ-_ PIE paragraph.pdf"
## [877] "TEJ-Guide-for-Rhetorical-Analysis.pdf"
## [878] "The fourth Reading Response.pdf"
## [879] "The Six-Word Memoir.docx"
## [880] "The_Rohingya_Crisis_Human_Rights_Issues_Policy_Con..._----_(Part_I_The_Rohingya_Refugees_in_Bangladesh).pdf"
## [881] "They Say_I Say templates (1).pdf"
## [882] "They Say_I Say templates (2).pdf"
## [883] "They Say_I Say templates.pdf"
## [884] "this_message_in_html.html"
## [885] "Titration Unknown HCl.pdf"
## [886] "To Millbrae Skilled Care (1).mp4"
## [887] "To Millbrae Skilled Care.mp4"
## [888] "torque_en (1).jar"
## [889] "Transcript-Bernie2019-speech (1).docx"
## [890] "Transcript-Bernie2019-speech.docx"
## [891] "transpose_VCF_data (1).html"
## [892] "transpose_VCF_data (2).html"
## [893] "transpose_VCF_data (3).html"
## [894] "transpose_VCF_data.html"
## [895] "transpose_VCF_data.Rmd"
## [896] "TRIPLE ENTRY JOURNAL (1).pages"
## [897] "TRIPLE ENTRY JOURNAL .pages"
## [898] "TRIPLE ENTRY JOURNAL .pdf"
## [899] "Triple-Entry-Journal-template (1).doc"
## [900] "Triple-Entry-Journal-template (2).doc"
## [901] "Triple-Entry-Journal-template (2).pages"
## [902] "Triple-Entry-Journal-template (3).doc"
## [903] "Triple-Entry-Journal-template (4).doc"
## [904] "Triple-Entry-Journal-template (5).doc"
## [905] "Triple-Entry-Journal-template-for-RA.doc"
## [906] "Triple-Entry-Journal-template.doc"
## [907] "tsis-aint-so.pdf"
## [908] "Understanding_the_Micropipette_Module_1 (1).docx"
## [909] "Understanding_the_Micropipette_Module_1.docx"
## [910] "Unit 2 Week 5 - Vocab for Rhythm.docx"
## [911] "Unit 2 Week 6 - Vocab for Rhythm 2.docx"
## [912] "Unit 3 Week 12 Rap 1 - Vocab (1).docx"
## [913] "Unit 3 Week 13 Rap 2 - Vocab.docx"
## [914] "Unit 4 - Vocab for Sound Assemblage (1).docx"
## [915] "Unit 6 Question 2.pdf"
## [916] "Unit_0 (1).pdf"
## [917] "Unit_0.pdf"
## [918] "Unit_1 (1).pdf"
## [919] "Unit_1.docx"
## [920] "Unit_1.pdf"
## [921] "Unit_11.doc"
## [922] "Unit_12.pdf"
## [923] "Unit_13.pdf"
## [924] "unit_2 (1).pdf"
## [925] "unit_2.pdf"
## [926] "Unit_3 (1).pdf"
## [927] "Unit_3.pdf"
## [928] "unnamed.jpg"
## [929] "Untitled (1).png"
## [930] "Untitled (2).png"
## [931] "Untitled document (1).pdf"
## [932] "Untitled document.pdf"
## [933] "Untitled.png"
## [934] "Uplifting Acoustic Background Music For Videos.mp3"
## [935] "Using Your Observation.docx"
## [936] "USW00093822-tavg-12-12-1895-2021.csv"
## [937] "VDB.txt"
## [938] "vegan_PCA_amino_acids-STUDENT.Rmd"
## [939] "vegan_pca_with_msleep-STUDENT (1).Rmd"
## [940] "vehiclewConstructors"
## [941] "vehiclewConstructors (1).zip"
## [942] "vehiclewConstructors.zip"
## [943] "Video.mov"
## [944] "VideoBeautyMovie 10.MP4"
## [945] "VideoBeautyMovie 11.MP4"
## [946] "VideoBeautyMovie 12.MP4"
## [947] "VideoBeautyMovie 2.MP4"
## [948] "VideoBeautyMovie 3.MP4"
## [949] "VideoBeautyMovie 4.MP4"
## [950] "VideoBeautyMovie 5.MP4"
## [951] "VideoBeautyMovie 6.MP4"
## [952] "VideoBeautyMovie 7.MP4"
## [953] "VideoBeautyMovie 8.MP4"
## [954] "VideoBeautyMovie 9.MP4"
## [955] "VideoBeautyMovie.MP4"
## [956] "Vocabulary Sheet - song form (1).docx"
## [957] "Vocabulary Sheet - song form (1).pages"
## [958] "Vocabulary Sheet - song form.docx"
## [959] "Vocabulary Sheet_ Week 7.pdf"
## [960] "Vocabulary Sheet_ Week 8 (1).pdf"
## [961] "Vocabulary Sheet_ Week 8.pdf"
## [962] "W8 Thu PDF reading#1_Wushuang.pdf"
## [963] "W8 Thu PDF reading#2_Xie Xiaoe.pdf"
## [964] "walsh2017morphology.csv"
## [965] "walsh2017morphology.RData"
## [966] "We Should All Be Feminists (1).pdf"
## [967] "We Should All Be Feminists (2).pdf"
## [968] "We Should All Be Feminists (3).pdf"
## [969] "We Should All Be Feminists.pdf"
## [970] "Webex.pkg"
## [971] "Week 10 Assignment - Short Composition with chords (1).docx"
## [972] "Week 10 Assignment - Short Composition with chords.docx"
## [973] "Week 10 Vocab - Pitch.docx"
## [974] "Week 10 Vocab Pitch.docx.pdf"
## [975] "Week 11 vocabulary.pdf"
## [976] "week 2 - musical vocab handout.pdf"
## [977] "Week 2(Part1).mp3"
## [978] "Week 5 Vocab Sheet.pdf"
## [979] "Week 6 Vocab_ Rhythm part 2.pdf"
## [980] "Week 7 Vocabulary Sheet.dotx"
## [981] "Week 8 Vocab.docx"
## [982] "week 9 vocabulary sheet.pdf"
## [983] "Week6 Mini Lecture Elasticity and Revenue.pdf"
## [984] "Week6 Mini Lecture Other Elasticities.pdf"
## [985] "Week6 Mini Lecture Price Elasticity of Demand.pdf"
## [986] "Weekly Time Management Schedule.xlsx"
## [987] "WK 11 Bio HW.docx"
## [988] "WK11Vocab-1 (1).docx"
## [989] "WK11Vocab-1.docx"
## [990] "working_directory_practice (1).Rmd"
## [991] "working_directory_practice.Rmd"
## [992] "Writing Process.pdf"
## [993] "Xiaoyi Zhu- Residency Reclassification.pdf"
## [994] "Xiaoyi Zhu-RA-ApplicationSpring.docx"
## [995] "xiuxiu_setup.exe"
## [996] "xiuxiu64_setup (1).exe"
## [997] "xiuxiu64_setup.exe"
## [998] "XYZ-Host_Range_Data_Card_Template.jpeg"
## [999] "Yates_Chapter_6_Notes_and_Answers.doc"
## [1000] "your grade calculator 0220.xlsx"
## [1001] "Zhu_Transcript_Unofficial.pdf"
## [1002] "Zhu-09.14-Asynch-Response.docx"
## [1003] "Zhu-09.21-Asynch-Response.docx"
## [1004] "Zhu-09.23-Asynch-Response.docx"
## [1005] "Zhu-10.12-Asynch-Response.docx"
## [1006] "Zhu-10.19-Asynch-Response.docx"
## [1007] "Zhu-10.21-Asynch-Response.docx"
## [1008] "Zhu-10.26-Asynch-Response.docx"
## [1009] "Zhu-10.28-Asynch-Response.docx"
## [1010] "Zhu-10.5-Asynch-Response.docx"
## [1011] "Zhu-10.7-Asynch-Response.docx"
## [1012] "Zhu-11.1&11.3-Asynch-Response.docx"
## [1013] "Zhu-11.2&11.4-Asynch-Response.docx"
## [1014] "Zhu-11.9&11.11-Asynch-Response.docx"
## [1015] "Zhu-8.31-asynch-response.docx"
## [1016] "Zoom.pkg"
## [1017] "居老师8图.jpeg"
## [1018] "布丁狗和他的小伙伴.mssf"
## [1019] "无标题文档 (1).pdf"
## [1020] "无标题文档.pdf"
## [1021] "爸妈W-2.pdf"
## [1022] "越长大越孤单（小时候）.pages"list.files(pattern = "vcf")## [1] "1.159051856-159301856.ALL.chr1_GRCh38.genotypes.20170504 (1).vcf.gz"
## [2] "1.159051856-159301856.ALL.chr1_GRCh38.genotypes.20170504.vcf.gz"
## [3] "all_loci-1.vcf"
## [4] "all_loci.vcf"
## [5] "code_checkpoint_vcfR.Rmd"Data preparation
TODO: Load Data
TODO: Load the data with vcfR::read.vcfR() into an object called snps
snps <- vcfR::read.vcfR("all_loci.vcf", convertNA = TRUE)## 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 processedTODO: Extract numeric genotype scores
TODO: Use vcfR::extract.gt to extract the numeric scores and save into an object called snps_num
snps_num <- vcfR::extract.gt(snps,
element = "GT",
IDtoRowNames = F,
as.numeric = T,
convertNA = T,
return.alleles = F)TODO: Transpose numeric genotype scores
TODO: Because data are formatted as genotype scores but SNPs are in columns and samples in row. To reformat them run the transpose function t() on snps_num. Save the result to an object called snaps_num_t.
snps_num_t <- t(snps_num) TODO: Use the data.frame() to turn snps_num_t into a dataframe and assign it to an object called snps_num_df.
snps_num_df <- data.frame(snps_num_t) TODO: Remove low-quality data
TODO: Load find_NAs() which is a function that will look for NAs in single column or vector, and give us the index values.
find_NAs <- function(x){
NAs_TF <- is.na(x)
i_NA <- which(NAs_TF == TRUE)
N_NA <- length(i_NA)
cat("Results:",N_NA, "NAs present\n.")
return(i_NA)
}TODO: for() loop to search for NAs
# N_rows
# number of rows (individuals)
N_rows <- nrow(snps_num_t)
# N_NA
# vector to hold output (number of NAs)
N_NA <- rep(x = 0, times = N_rows)
# N_SNPs
# total number of columns (SNPs)
N_SNPs <- ncol(snps_num_t)
# the for() loop
for(i in 1:N_rows){
# for each row, find the location of
## NAs with snps_num_t()
i_NA <- find_NAs(snps_num_t[i,])
# then determine how many NAs
## with length()
N_NA_i <- length(i_NA)
# then save the output to
## our storage vector
N_NA[i] <- N_NA_i
}## Results: 28 NAs present
## .Results: 20 NAs present
## .Results: 28 NAs present
## .Results: 24 NAs present
## .Results: 23 NAs present
## .Results: 63 NAs present
## .Results: 51 NAs present
## .Results: 38 NAs present
## .Results: 34 NAs present
## .Results: 24 NAs present
## .Results: 48 NAs present
## .Results: 21 NAs present
## .Results: 42 NAs present
## .Results: 78 NAs present
## .Results: 45 NAs present
## .Results: 21 NAs present
## .Results: 42 NAs present
## .Results: 34 NAs present
## .Results: 66 NAs present
## .Results: 54 NAs present
## .Results: 59 NAs present
## .Results: 52 NAs present
## .Results: 47 NAs present
## .Results: 31 NAs present
## .Results: 63 NAs present
## .Results: 40 NAs present
## .Results: 40 NAs present
## .Results: 22 NAs present
## .Results: 60 NAs present
## .Results: 48 NAs present
## .Results: 961 NAs present
## .Results: 478 NAs present
## .Results: 59 NAs present
## .Results: 26 NAs present
## .Results: 285 NAs present
## .Results: 409 NAs present
## .Results: 1140 NAs present
## .Results: 600 NAs present
## .Results: 1905 NAs present
## .Results: 25 NAs present
## .Results: 1247 NAs present
## .Results: 23 NAs present
## .Results: 750 NAs present
## .Results: 179 NAs present
## .Results: 433 NAs present
## .Results: 123 NAs present
## .Results: 65 NAs present
## .Results: 49 NAs present
## .Results: 192 NAs present
## .Results: 433 NAs present
## .Results: 66 NAs present
## .Results: 597 NAs present
## .Results: 1891 NAs present
## .Results: 207 NAs present
## .Results: 41 NAs present
## .Results: 268 NAs present
## .Results: 43 NAs present
## .Results: 110 NAs present
## .Results: 130 NAs present
## .Results: 90 NAs present
## .Results: 271 NAs present
## .Results: 92 NAs present
## .Results: 103 NAs present
## .Results: 175 NAs present
## .Results: 31 NAs present
## .Results: 66 NAs present
## .Results: 64 NAs present
## .Results: 400 NAs present
## .Results: 192 NAs present
## .Results: 251 NAs present
## .Results: 69 NAs present
## .Results: 58 NAs present
## .TODO: Check if any row has >50% NAs and make a plot with LOBF
# 50% of N_SNPs
cutoff50 <- N_SNPs*0.5
hist(N_NA)
abline(v = cutoff50,
col = 2,
lwd = 2,
lty = 2)
TODO: Calculate the percentage and mins the roll that has >50% NAs(i_NA_50percent)
percent_NA <- N_NA/N_SNPs*100
# Call which() on percent_NA
i_NA_50percent <- which(percent_NA > 50)
snps_num_t02 <- snps_num_t[-i_NA_50percent, ]TODO: Regular Expression
TODO: Make the sample names easier to see using gsub()
row_names <- row.names(snps_num_t02) # Key
row_names02 <- gsub("sample_","",row_names)
sample_id <- gsub("^([ATCG]*)(_)(.*)",
"\\3",
row_names02)
pop_id <- gsub("[01-9]*",
"",
sample_id)
table(pop_id) ## pop_id
## Alt Cau Div Nel Sub
## 15 12 15 15 11TODO: Omit invariant features
TODO: Load invar_omit() function
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)
}
snps_no_invar <- invar_omit(snps_num_t02) ## Dataframe of dim 68 1929 processed...
## 591 columns removedTODO: Imputation of NAs
TODO: Load imputation function
snps_noNAs <- snps_no_invar
N_col <- ncol(snps_no_invar)
for(i in 1:N_col){
# get the current column
column_i <- snps_noNAs[, i]
# get the mean of the current column
mean_i <- mean(column_i, na.rm = TRUE)
# get the NAs in the current column
NAs_i <- which(is.na(column_i))
# record the number of NAs
N_NAs <- length(NAs_i)
# replace the NAs in the current column
column_i[NAs_i] <- mean_i
# replace the original column with the
## updated columns
snps_noNAs[, i] <- column_i
}Save the data
Save the data as a .csv file which can be loaded again later.
write.csv(snps_noNAs, file = "SNPs_cleaned.csv",
row.names = F)Check for the presence of the file with list.files()
list.files(pattern = ".csv")## [1] "SNPs_cleaned.csv"
## [2] "USW00093822-tavg-12-12-1895-2021.csv"
## [3] "walsh2017morphology.csv"Next steps:
In Part 2, we will re-load the SNPs_cleaned.csv file and
carry an an analysis with PCA.