Gc PCA LD Trimmed
Ryan Stratychuk
March 26, 2018
## SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)##
## Attaching package: 'dplyr'## The following objects are masked from 'package:stats':
##
## filter, lag## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, unionPruning SNPs By LD
Using the package SNPRelate to easily work with data and provide PCA analysis.
First the VCF for Gc_HQ.recode must be converted to the GDS filetype and opened
## VCF Format ==> SNP GDS Format
## Method: exacting biallelic SNPs
## Number of samples: 267
## Parsing "C:/Users/Ryan/Desktop/TRIA-GEA/Species Data Files/VCFs/Gc_HQ.recode.vcf_STATS/Gc_HQ.recode.vcf" ...
## import 17367 variants.
## + genotype { Bit2 267x17367, 1.1M } *
## Optimize the access efficiency ...
## Clean up the fragments of GDS file:
## open the file 'Gc_HQ.recode.gds' (1.2M)
## # of fragments: 42
## save to 'Gc_HQ.recode.gds.tmp'
## rename 'Gc_HQ.recode.gds.tmp' (1.2M, reduced: 264B)
## # of fragments: 20## The file name: C:\Users\Ryan\Desktop\TRIA-PCA\Gc_HQ.recode.gds
## The total number of samples: 267
## The total number of SNPs: 17367
## SNP genotypes are stored in SNP-major mode (Sample X SNP).Then the pruning by LD can begin. The function use will recursively remove SNPs within a sliding window based on pairwise correlation. The initial threshold distance between SNPs, the LD Threshold, is 0.2. Pruning is important to reduce redundancy in the dataset and reduce chromosomal artifacts from influencing the analyses downstream.
snpset <- snpgdsLDpruning(genofile , ld.threshold = 0.2, autosome.only = FALSE)## SNP pruning based on LD:
## Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
## Working space: 267 samples, 17,367 SNPs
## using 1 (CPU) core
## sliding window: 500,000 basepairs, Inf SNPs
## |LD| threshold: 0.2
## method: composite
## Chromosome GCLVSC_067: 25.00%, 2/8
## Chromosome GCLVSC_082: 5.16%, 28/543
## Chromosome GCLVSC_089: 5.99%, 38/634
## Chromosome GCLVSC_097: 5.86%, 79/1,349
## Chromosome GCLVSC_099: 100.00%, 1/1
## Chromosome GCLVSC_105: 50.00%, 1/2
## Chromosome GCLVSC_108: 4.50%, 50/1,111
## Chromosome GCLVSC_113: 4.34%, 93/2,141
## Chromosome GCLVSC_117: 50.00%, 4/8
## Chromosome GCLVSC_124: 8.79%, 8/91
## Chromosome GCLVSC_132: 4.18%, 29/693
## Chromosome GCLVSC_136: 50.00%, 1/2
## Chromosome GCLVSC_140: 4.32%, 125/2,893
## Chromosome GCLVSC_142: 7.24%, 11/152
## Chromosome GCLVSC_144: 4.69%, 74/1,577
## Chromosome GCLVSC_146: 5.45%, 12/220
## Chromosome GCLVSC_147: 50.00%, 1/2
## Chromosome GCLVSC_156: 5.23%, 47/899
## Chromosome GCLVSC_160: 5.42%, 18/332
## Chromosome GCLVSC_161: 3.62%, 23/636
## Chromosome GCLVSC_162: 75.00%, 3/4
## Chromosome GCLVSC_164: 100.00%, 1/1
## Chromosome GCLVSC_167: 4.45%, 57/1,282
## Chromosome GCLVSC_168: 5.67%, 27/476
## Chromosome GCLVSC_173: 4.75%, 69/1,453
## Chromosome GCLVSC_179: 4.52%, 38/840
## Chromosome GCLVSC_180: 36.36%, 4/11
## Chromosome GCLVSC_200: 100.00%, 1/1
## Chromosome GCLVSC_272: 40.00%, 2/5
## 847 markers are selected in total.names(snpset)## [1] "chrGCLVSC_067" "chrGCLVSC_082" "chrGCLVSC_089" "chrGCLVSC_097"
## [5] "chrGCLVSC_099" "chrGCLVSC_105" "chrGCLVSC_108" "chrGCLVSC_113"
## [9] "chrGCLVSC_117" "chrGCLVSC_124" "chrGCLVSC_132" "chrGCLVSC_136"
## [13] "chrGCLVSC_140" "chrGCLVSC_142" "chrGCLVSC_144" "chrGCLVSC_146"
## [17] "chrGCLVSC_147" "chrGCLVSC_156" "chrGCLVSC_160" "chrGCLVSC_161"
## [21] "chrGCLVSC_162" "chrGCLVSC_164" "chrGCLVSC_167" "chrGCLVSC_168"
## [25] "chrGCLVSC_173" "chrGCLVSC_179" "chrGCLVSC_180" "chrGCLVSC_200"
## [29] "chrGCLVSC_272"snpset.id <- unlist(snpset)Next the PCA is conducted.
pca <- snpgdsPCA(genofile, snp.id = snpset.id, num.thread = 2, autosome.only = FALSE)## Principal Component Analysis (PCA) on genotypes:
## Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
## Working space: 267 samples, 847 SNPs
## using 2 (CPU) cores
## PCA: the sum of all selected genotypes (0,1,2) = 410436
## CPU capabilities: Double-Precision SSE2
## Mon Mar 26 12:34:19 2018 (internal increment: 1332)
##
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
## Mon Mar 26 12:34:19 2018 Begin (eigenvalues and eigenvectors)
## Mon Mar 26 12:34:19 2018 Done.The proportion of variance explained by the eigenvectors can be calculated from this
## [1] 6.31 5.06 3.12 2.33 2.15 2.11Then we can make a dataframe the contains the eigenvector values for each sample
tab <- data.frame(sample.id = pca$sample.id,
EV1 = pca$eigenvect[,1],
EV2 = pca$eigenvect[,2],
stringsAsFactors = FALSE)
head(tab)## sample.id EV1
## 1 /mnt/bulleit/arnaud/Plate2_6/ss100_Gc_Plate02_A01.sorted.bam -0.01050290
## 2 /mnt/bulleit/arnaud/Plate2_6/ss139_Gc_Plate02_B01.sorted.bam -0.01739326
## 3 /mnt/bulleit/arnaud/Plate2_6/ss169_Gc_Plate02_D01.sorted.bam -0.01189309
## 4 /mnt/bulleit/arnaud/Plate2_6/ss180_Gc_Plate02_E01.sorted.bam -0.01187445
## 5 /mnt/bulleit/arnaud/Plate2_6/ss205_Gc_Plate02_G01.sorted.bam -0.01009028
## 6 /mnt/bulleit/arnaud/Plate2_6/ss217_Gc_Plate02_A02.sorted.bam -0.01188969
## EV2
## 1 -0.004921567
## 2 -0.008402154
## 3 -0.002792606
## 4 -0.005514651
## 5 -0.003783535
## 6 -0.003737967Then it is time to draw the PCA plot
plot(tab$EV2, tab$EV1, xlab="eigenvector 2", ylab="eigenvector 1")
title(main = "Gc PCA LD Trimmed")
Using dplyr we can easily filter and arrange the dataframe of values to find which samples belong to what groups.
## # A tibble: 3 x 3
## sample.id EV1 EV2
## <chr> <dbl> <dbl>
## 1 /mnt/bulleit/arnaud/Plate7_9/TRIA129_Gc_Plate07_G07.sorted~ 0.486 -0.341
## 2 /mnt/bulleit/arnaud/Plate2_6/TRIA200_Gc_Plate03_E02.sorted~ 0.468 -0.325
## 3 /mnt/bulleit/arnaud/Plate7_9/TRIA286_Gc_Plate07_H07.sorted~ 0.458 -0.317## # A tibble: 257 x 3
## sample.id EV1 EV2
## <chr> <dbl> <dbl>
## 1 /mnt/bulleit/arnaud/Plate2_6/ss139_Gc_Plate02_B01.~ -0.0174 -8.40e-3
## 2 /mnt/bulleit/arnaud/Plate2_6/ss382_Gc_Plate02_C03.~ -0.0150 -8.39e-3
## 3 /mnt/bulleit/arnaud/Plate2_6/TRIA477_Gc_Plate06_C0~ -0.0160 -8.07e-3
## 4 /mnt/bulleit/arnaud/Plate1/Merged/TRIA68_Gc_Plate0~ -0.0157 -8.07e-3
## 5 /mnt/bulleit/arnaud/Plate2_6/TRIA482_Gc_Plate03_A0~ -0.0162 -8.04e-3
## 6 /mnt/bulleit/arnaud/Plate1/Merged/ss272_Gc_Plate01~ -0.0141 -7.95e-3
## 7 /mnt/bulleit/arnaud/Plate2_6/ss423_Gc_Plate02_E04.~ -0.0172 -7.91e-3
## 8 /mnt/bulleit/arnaud/Plate7_9/ss499_Gc_Plate07_H06.~ -0.0155 -7.85e-3
## 9 /mnt/bulleit/arnaud/Plate1/Merged/ss273_Gc_Plate01~ -0.0141 -7.81e-3
## 10 /mnt/bulleit/arnaud/Plate2_6/TRIA69_Gc_Plate02_A06~ -0.0141 -7.72e-3
## 11 /mnt/bulleit/arnaud/Plate2_6/ss396_Gc_Plate02_G03.~ -0.0150 -7.53e-3
## 12 /mnt/bulleit/arnaud/Plate2_6/TRIA241_Gc_Plate03_D0~ -0.0137 -7.48e-3
## 13 /mnt/bulleit/arnaud/Plate2_6/TRIA242_Gc_Plate03_E0~ -0.0137 -7.48e-3
## 14 /mnt/bulleit/arnaud/Plate2_6/TRIA243_Gc_Plate03_F0~ -0.0137 -7.48e-3
## 15 /mnt/bulleit/arnaud/Plate1/Merged/TRIA105_Gc_Plate~ -0.0133 -7.43e-3
## 16 /mnt/bulleit/arnaud/Plate2_6/ss333_Gc_Plate02_H02.~ -0.0144 -7.27e-3
## 17 /mnt/bulleit/arnaud/Plate2_6/ss383_Gc_Plate02_D03.~ -0.0141 -7.18e-3
## 18 /mnt/bulleit/arnaud/Plate1/Merged/ss270_Gc_Plate01~ -0.0132 -7.16e-3
## 19 /mnt/bulleit/arnaud/Plate7_9/TRIA381_Gc_Plate07_F0~ -0.0117 -7.12e-3
## 20 /mnt/bulleit/arnaud/Plate2_6/ss410_Gc_Plate06_B01.~ -0.0135 -7.09e-3
## 21 /mnt/bulleit/arnaud/Plate2_6/TRIA277_Gc_Plate03_F0~ -0.0133 -6.98e-3
## 22 /mnt/bulleit/arnaud/Plate2_6/TRIA81_Gc_Plate02_C07~ -0.0133 -6.98e-3
## 23 /mnt/bulleit/arnaud/Plate2_6/TRIA838_Gc_Plate03_H1~ -0.0110 -6.94e-3
## 24 /mnt/bulleit/arnaud/Plate7_9/ss421_Gc_Plate07_C05.~ -0.0143 -6.87e-3
## 25 /mnt/bulleit/arnaud/Plate2_6/TRIA89_Gc_Plate02_G07~ -0.0143 -6.86e-3
## 26 /mnt/bulleit/arnaud/merged_bam/ss269_Gc_merged_sor~ -0.0130 -6.80e-3
## 27 /mnt/bulleit/arnaud/Plate2_6/TRIA777_Gc_Plate03_B1~ -0.0140 -6.78e-3
## 28 /mnt/bulleit/arnaud/Plate2_6/TRIA339_Gc_Plate03_G0~ -0.0140 -6.76e-3
## 29 /mnt/bulleit/arnaud/Plate1/Merged/ss256_Gc_Plate01~ -0.0122 -6.75e-3
## 30 /mnt/bulleit/arnaud/Plate2_6/TRIA173_Gc_Plate02_B1~ -0.0136 -6.74e-3
## 31 /mnt/bulleit/arnaud/Plate2_6/TRIA197_Gc_Plate03_C0~ -0.0132 -6.73e-3
## 32 /mnt/bulleit/arnaud/Plate2_6/TRIA193_Gc_Plate03_B0~ -0.0132 -6.73e-3
## 33 /mnt/bulleit/arnaud/Plate2_6/TRIA418_Gc_Plate03_C0~ -0.0125 -6.69e-3
## 34 /mnt/bulleit/arnaud/Plate2_6/TRIA215_Gc_Plate03_G0~ -0.0104 -6.68e-3
## 35 /mnt/bulleit/arnaud/Plate1/Merged/TRIA196_Gc_Plate~ -0.0121 -6.67e-3
## 36 /mnt/bulleit/arnaud/Plate2_6/TRIA109_Gc_Plate02_F0~ -0.0141 -6.65e-3
## 37 /mnt/bulleit/arnaud/Plate7_9/TRIA359_Gc_Plate07_D0~ -0.0155 -6.65e-3
## 38 /mnt/bulleit/arnaud/Plate1/Merged/TRIA158_Gc_Plate~ -0.0127 -6.60e-3
## 39 /mnt/bulleit/arnaud/Plate2_6/TRIA172_Gc_Plate02_A1~ -0.0129 -6.60e-3
## 40 /mnt/bulleit/arnaud/Plate7_9/TRIA93_Gc_Plate07_D07~ -0.0129 -6.60e-3
## 41 /mnt/bulleit/arnaud/Plate1/Merged/ss31_Gc_Plate01_~ -0.0137 -6.58e-3
## 42 /mnt/bulleit/arnaud/Plate2_6/ss77_Gc_Plate06_A01.s~ -0.0122 -6.58e-3
## 43 /mnt/bulleit/arnaud/Plate1/Merged/TRIA65_Gc_Plate0~ -0.0126 -6.57e-3
## 44 /mnt/bulleit/arnaud/Plate7_9/ss395_Gc_Plate07_H04.~ -0.0130 -6.56e-3
## 45 /mnt/bulleit/arnaud/Plate2_6/TRIA73_Gc_Plate02_E06~ -0.0139 -6.54e-3
## 46 /mnt/bulleit/arnaud/Plate2_6/TRIA135_Gc_Plate02_A1~ -0.0139 -6.54e-3
## 47 /mnt/bulleit/arnaud/Plate1/Merged/ss223_Gc_Plate01~ -0.0122 -6.52e-3
## 48 /mnt/bulleit/arnaud/Plate2_6/ss384_Gc_Plate02_E03.~ -0.0131 -6.45e-3
## 49 /mnt/bulleit/arnaud/Plate2_6/TRIA131_Gc_Plate02_G0~ -0.0124 -6.44e-3
## 50 /mnt/bulleit/arnaud/Plate2_6/TRIA198_Gc_Plate03_D0~ -0.0126 -6.33e-3
## 51 /mnt/bulleit/arnaud/Plate7_9/TRIA114_Gc_Plate08_A0~ -0.0126 -6.33e-3
## 52 /mnt/bulleit/arnaud/Plate2_6/TRIA110_Gc_Plate02_G0~ -0.0126 -6.33e-3
## 53 /mnt/bulleit/arnaud/Plate2_6/TRIA783_Gc_Plate03_F1~ -0.0137 -6.31e-3
## 54 /mnt/bulleit/arnaud/Plate2_6/TRIA281_Gc_Plate03_H0~ -0.0129 -6.31e-3
## 55 /mnt/bulleit/arnaud/Plate7_9/ss481_Gc_Plate07_E06.~ -0.0131 -6.29e-3
## 56 /mnt/bulleit/arnaud/Plate2_6/TRIA284_Gc_Plate03_A0~ -0.0126 -6.29e-3
## 57 /mnt/bulleit/arnaud/Plate2_6/ss254_Gc_Plate02_D02.~ -0.0135 -6.26e-3
## 58 /mnt/bulleit/arnaud/Plate2_6/TRIA182_Gc_Plate03_A0~ -0.0129 -6.25e-3
## 59 /mnt/bulleit/arnaud/Plate7_9/ss142_Gc_Plate07_F02.~ -0.0115 -6.23e-3
## 60 /mnt/bulleit/arnaud/Plate2_6/TRIA305_Gc_Plate03_F0~ -0.0129 -6.20e-3
## 61 /mnt/bulleit/arnaud/Plate2_6/TRIA253_Gc_Plate03_G0~ -0.0120 -6.19e-3
## 62 /mnt/bulleit/arnaud/Plate2_6/TRIA638_Gc_Plate03_F0~ -0.0130 -6.18e-3
## 63 /mnt/bulleit/arnaud/Plate2_6/ss401_Gc_Plate02_A04.~ -0.0152 -6.16e-3
## 64 /mnt/bulleit/arnaud/Plate2_6/TRIA867_Gc_Plate03_D1~ -0.0134 -6.16e-3
## 65 /mnt/bulleit/arnaud/Plate2_6/TRIA968_Gc_Plate04_G0~ -0.0129 -6.10e-3
## 66 /mnt/bulleit/arnaud/Plate2_6/TRIA122_Gc_Plate02_C0~ -0.0119 -6.08e-3
## 67 /mnt/bulleit/arnaud/Plate2_6/TRIA140_Gc_Plate02_E1~ -0.0119 -6.08e-3
## 68 /mnt/bulleit/arnaud/Plate7_9/ss437_Gc_Plate07_F05.~ -0.0121 -6.08e-3
## 69 /mnt/bulleit/arnaud/Plate1/Merged/TRIA101_Gc_Plate~ -0.0130 -6.05e-3
## 70 /mnt/bulleit/arnaud/Plate2_6/TRIA298_Gc_Plate03_D0~ -0.0130 -6.00e-3
## 71 /mnt/bulleit/arnaud/Plate2_6/TRIA212_Gc_Plate03_F0~ -0.0133 -6.00e-3
## 72 /mnt/bulleit/arnaud/Plate7_9/ss436_Gc_Plate07_E05.~ -0.0124 -5.99e-3
## 73 /mnt/bulleit/arnaud/Plate2_6/TRIA272_Gc_Plate03_C0~ -0.0122 -5.93e-3
## 74 /mnt/bulleit/arnaud/Plate2_6/TRIA151_Gc_Plate02_B1~ -0.0118 -5.91e-3
## 75 /mnt/bulleit/arnaud/Plate7_9/ss390_Gc_Plate07_E04.~ -0.0146 -5.91e-3
## 76 /mnt/bulleit/arnaud/Plate2_6/TRIA139_Gc_Plate02_D1~ -0.0126 -5.91e-3
## 77 /mnt/bulleit/arnaud/Plate2_6/TRIA223_Gc_Plate03_A0~ -0.0126 -5.91e-3
## 78 /mnt/bulleit/arnaud/Plate2_6/TRIA116_Gc_Plate02_B0~ -0.0131 -5.89e-3
## 79 /mnt/bulleit/arnaud/Plate2_6/TRIA233_Gc_Plate03_C0~ -0.0127 -5.88e-3
## 80 /mnt/bulleit/arnaud/Plate1/Merged/ss266_Gc_Plate01~ -0.0111 -5.87e-3
## 81 /mnt/bulleit/arnaud/Plate2_6/TRIA176_Gc_Plate02_E1~ -0.0124 -5.86e-3
## 82 /mnt/bulleit/arnaud/Plate1/Merged/TRIA100_Gc_Plate~ -0.0121 -5.85e-3
## 83 /mnt/bulleit/arnaud/Plate2_6/TRIA803_Gc_Plate03_C1~ -0.0129 -5.84e-3
## 84 /mnt/bulleit/arnaud/Plate2_6/TRIA76_Gc_Plate02_H06~ -0.0116 -5.83e-3
## 85 /mnt/bulleit/arnaud/Plate2_6/TRIA296_Gc_Plate06_F0~ -0.0128 -5.81e-3
## 86 /mnt/bulleit/arnaud/Plate2_6/TRIA187_Gc_Plate03_F0~ -0.0125 -5.81e-3
## 87 /mnt/bulleit/arnaud/Plate2_6/TRIA103_Gc_Plate06_H0~ -0.0123 -5.79e-3
## 88 /mnt/bulleit/arnaud/Plate7_9/ss106_Gc_Plate07_G01.~ -0.0118 -5.78e-3
## 89 /mnt/bulleit/arnaud/Plate2_6/TRIA99_Gc_Plate02_C08~ -0.0113 -5.78e-3
## 90 /mnt/bulleit/arnaud/Plate1/Merged/ss271_Gc_Plate01~ -0.0129 -5.76e-3
## 91 /mnt/bulleit/arnaud/Plate2_6/TRIA970_Gc_Plate04_H0~ -0.0118 -5.76e-3
## 92 /mnt/bulleit/arnaud/Plate2_6/TRIA144_Gc_Plate02_G1~ -0.0113 -5.74e-3
## 93 /mnt/bulleit/arnaud/Plate2_6/TRIA98_Gc_Plate02_B08~ -0.0121 -5.70e-3
## 94 /mnt/bulleit/arnaud/Plate2_6/TRIA1008_Gc_Plate04_G~ -0.0117 -5.67e-3
## 95 /mnt/bulleit/arnaud/Plate2_6/TRIA192_Gc_Plate03_A0~ -0.0132 -5.66e-3
## 96 /mnt/bulleit/arnaud/Plate7_9/ss249_Gc_Plate07_E03.~ -0.0122 -5.66e-3
## 97 /mnt/bulleit/arnaud/Plate7_9/ss140_Gc_Plate07_D02.~ -0.0122 -5.66e-3
## 98 /mnt/bulleit/arnaud/Plate2_6/TRIA74_Gc_Plate02_F06~ -0.0120 -5.64e-3
## 99 /mnt/bulleit/arnaud/Plate1/Merged/ss243_Gc_Plate01~ -0.0113 -5.61e-3
## 100 /mnt/bulleit/arnaud/Plate2_6/ss459_Gc_Plate02_H04.~ -0.0122 -5.61e-3
## 101 /mnt/bulleit/arnaud/Plate2_6/TRIA72_Gc_Plate02_D06~ -0.0119 -5.57e-3
## 102 /mnt/bulleit/arnaud/Plate2_6/TRIA413_Gc_Plate03_B0~ -0.0132 -5.56e-3
## 103 /mnt/bulleit/arnaud/Plate2_6/TRIA79_Gc_Plate02_A07~ -0.0121 -5.52e-3
## 104 /mnt/bulleit/arnaud/Plate1/Merged/ss274_Gc_Plate01~ -0.0117 -5.52e-3
## 105 /mnt/bulleit/arnaud/Plate2_6/ss180_Gc_Plate02_E01.~ -0.0119 -5.51e-3
## 106 /mnt/bulleit/arnaud/Plate1/Merged/ss6_Gc_Plate01_H~ -0.0118 -5.50e-3
## 107 /mnt/bulleit/arnaud/Plate2_6/TRIA219_Gc_Plate03_H0~ -0.0123 -5.50e-3
## 108 /mnt/bulleit/arnaud/Plate2_6/TRIA174_Gc_Plate02_C1~ -0.0119 -5.50e-3
## 109 /mnt/bulleit/arnaud/Plate2_6/TRIA947_Gc_Plate04_B0~ -0.0121 -5.49e-3
## 110 /mnt/bulleit/arnaud/Plate2_6/ss427_Gc_Plate02_F04.~ -0.0117 -5.49e-3
## 111 /mnt/bulleit/arnaud/Plate2_6/TRIA180_Gc_Plate02_G1~ -0.0111 -5.49e-3
## 112 /mnt/bulleit/arnaud/Plate1/Merged/TRIA107_Gc_Plate~ -0.0119 -5.49e-3
## 113 /mnt/bulleit/arnaud/Plate1/Merged/ss222_Gc_Plate01~ -0.0124 -5.47e-3
## 114 /mnt/bulleit/arnaud/Plate7_9/ss166_Gc_Plate07_G02.~ -0.0124 -5.47e-3
## 115 /mnt/bulleit/arnaud/Plate7_9/ss209_Gc_Plate07_C03.~ -0.0116 -5.46e-3
## 116 /mnt/bulleit/arnaud/Plate2_6/TRIA837_Gc_Plate03_G1~ -0.0135 -5.45e-3
## 117 /mnt/bulleit/arnaud/Plate2_6/TRIA154_Gc_Plate02_C1~ -0.0109 -5.44e-3
## 118 /mnt/bulleit/arnaud/Plate1/Merged/TRIA67_Gc_Plate0~ -0.00870 -5.40e-3
## 119 /mnt/bulleit/arnaud/Plate2_6/TRIA148_Gc_Plate02_A1~ -0.00924 -5.39e-3
## 120 /mnt/bulleit/arnaud/Plate1/Merged/TRIA160_Gc_Plate~ -0.00923 -5.37e-3
## 121 /mnt/bulleit/arnaud/Plate2_6/TRIA45_Gc_Plate06_F01~ -0.0119 -5.36e-3
## 122 /mnt/bulleit/arnaud/Plate2_6/ss397_Gc_Plate02_H03.~ -0.0115 -5.36e-3
## 123 /mnt/bulleit/arnaud/Plate7_9/ss124_Gc_Plate07_H01.~ -0.0113 -5.35e-3
## 124 /mnt/bulleit/arnaud/Plate1/Merged/TRIA199_Gc_Plate~ -0.0124 -5.34e-3
## 125 /mnt/bulleit/arnaud/Plate1/Merged/ss268_Gc_Plate01~ -0.0126 -5.27e-3
## 126 /mnt/bulleit/arnaud/Plate2_6/TRIA185_Gc_Plate03_D0~ -0.0110 -5.25e-3
## 127 /mnt/bulleit/arnaud/Plate7_9/TRIA396_Gc_Plate07_A1~ -0.0114 -5.18e-3
## 128 /mnt/bulleit/arnaud/Plate2_6/TRIA293_Gc_Plate03_C0~ -0.00948 -5.16e-3
## 129 /mnt/bulleit/arnaud/Plate2_6/TRIA431_Gc_Plate03_E0~ -0.0134 -5.13e-3
## 130 /mnt/bulleit/arnaud/Plate1/Merged/TRIA295_Gc_Plate~ -0.0114 -5.12e-3
## 131 /mnt/bulleit/arnaud/Plate1/Merged/ss255_Gc_Plate01~ -0.0112 -5.12e-3
## 132 /mnt/bulleit/arnaud/Plate2_6/TRIA958_Gc_Plate04_E0~ -0.0116 -5.10e-3
## 133 /mnt/bulleit/arnaud/Plate2_6/TRIA273_Gc_Plate03_D0~ -0.00795 -5.10e-3
## 134 /mnt/bulleit/arnaud/Plate7_9/ss285_Gc_Plate07_B04.~ -0.0123 -5.09e-3
## 135 /mnt/bulleit/arnaud/Plate2_6/TRIA945_Gc_Plate04_A0~ -0.0115 -5.09e-3
## 136 /mnt/bulleit/arnaud/Plate2_6/TRIA71_Gc_Plate02_C06~ -0.0113 -5.08e-3
## 137 /mnt/bulleit/arnaud/Plate2_6/TRIA559_Gc_Plate03_F0~ -0.0108 -5.07e-3
## 138 /mnt/bulleit/arnaud/Plate2_6/TRIA188_Gc_Plate03_G0~ -0.00996 -5.07e-3
## 139 /mnt/bulleit/arnaud/Plate2_6/TRIA86_Gc_Plate02_F07~ -0.0105 -5.05e-3
## 140 /mnt/bulleit/arnaud/Plate2_6/ss414_Gc_Plate02_D04.~ -0.0128 -5.04e-3
## 141 /mnt/bulleit/arnaud/Plate7_9/ss261_Gc_Plate07_A04.~ -0.0121 -5.03e-3
## 142 /mnt/bulleit/arnaud/Plate2_6/ss404_Gc_Plate02_B04.~ -0.0107 -5.03e-3
## 143 /mnt/bulleit/arnaud/Plate2_6/TRIA118_Gc_Plate06_A0~ -0.0112 -5.01e-3
## 144 /mnt/bulleit/arnaud/Plate2_6/TRIA83_Gc_Plate02_D07~ -0.0125 -4.95e-3
## 145 /mnt/bulleit/arnaud/Plate2_6/TRIA186_Gc_Plate03_E0~ -0.0129 -4.94e-3
## 146 /mnt/bulleit/arnaud/Plate2_6/TRIA70_Gc_Plate02_B06~ -0.0119 -4.93e-3
## 147 /mnt/bulleit/arnaud/Plate2_6/ss100_Gc_Plate02_A01.~ -0.0105 -4.92e-3
## 148 /mnt/bulleit/arnaud/Plate7_9/TRIA662_Gc_Plate09_E0~ -0.0107 -4.92e-3
## 149 /mnt/bulleit/arnaud/Plate2_6/TRIA130_Gc_Plate02_F0~ -0.0107 -4.91e-3
## 150 /mnt/bulleit/arnaud/Plate7_9/TRIA126_Gc_Plate07_F0~ -0.0107 -4.91e-3
## 151 /mnt/bulleit/arnaud/Plate7_9/ss476_Gc_Plate07_C06.~ -0.0149 -4.91e-3
## 152 /mnt/bulleit/arnaud/Plate2_6/TRIA112_Gc_Plate02_H0~ -0.0109 -4.89e-3
## 153 /mnt/bulleit/arnaud/Plate2_6/TRIA123_Gc_Plate02_D0~ -0.0109 -4.89e-3
## 154 /mnt/bulleit/arnaud/Plate2_6/TRIA1000_Gc_Plate04_F~ -0.0115 -4.87e-3
## 155 /mnt/bulleit/arnaud/Plate2_6/TRIA488_Gc_Plate03_B0~ -0.0103 -4.87e-3
## 156 /mnt/bulleit/arnaud/Plate2_6/TRIA165_Gc_Plate02_D1~ -0.0119 -4.83e-3
## 157 /mnt/bulleit/arnaud/Plate2_6/TRIA784_Gc_Plate03_G1~ -0.0116 -4.83e-3
## 158 /mnt/bulleit/arnaud/Plate2_6/TRIA166_Gc_Plate02_E1~ -0.0112 -4.81e-3
## 159 /mnt/bulleit/arnaud/Plate2_6/TRIA228_Gc_Plate03_B0~ -0.0105 -4.80e-3
## 160 /mnt/bulleit/arnaud/Plate2_6/TRIA802_Gc_Plate03_B1~ -0.0111 -4.79e-3
## 161 /mnt/bulleit/arnaud/Plate2_6/TRIA171_Gc_Plate02_H1~ -0.0117 -4.79e-3
## 162 /mnt/bulleit/arnaud/Plate2_6/TRIA781_Gc_Plate03_E1~ -0.0118 -4.78e-3
## 163 /mnt/bulleit/arnaud/Plate2_6/ss498_Gc_Plate02_E05.~ -0.0120 -4.75e-3
## 164 /mnt/bulleit/arnaud/Plate2_6/TRIA780_Gc_Plate03_D1~ -0.0115 -4.69e-3
## 165 /mnt/bulleit/arnaud/Plate7_9/ss391_Gc_Plate07_F04.~ -0.0137 -4.64e-3
## 166 /mnt/bulleit/arnaud/Plate7_9/TRIA401_Gc_Plate07_B1~ -0.0119 -4.61e-3
## 167 /mnt/bulleit/arnaud/Plate2_6/TRIA403_Gc_Plate03_H0~ -0.0119 -4.60e-3
## 168 /mnt/bulleit/arnaud/Plate2_6/ss278_Gc_Plate02_G02.~ -0.0113 -4.60e-3
## 169 /mnt/bulleit/arnaud/Plate7_9/TRIA385_Gc_Plate07_G0~ -0.0119 -4.60e-3
## 170 /mnt/bulleit/arnaud/Plate2_6/TRIA190_Gc_Plate03_H0~ -0.00992 -4.56e-3
## 171 /mnt/bulleit/arnaud/Plate2_6/TRIA146_Gc_Plate02_H1~ -0.00992 -4.56e-3
## 172 /mnt/bulleit/arnaud/Plate1/Merged/TRIA156_Gc_Plate~ -0.0102 -4.56e-3
## 173 /mnt/bulleit/arnaud/Plate1/Merged/TRIA157_Gc_Plate~ -0.0102 -4.56e-3
## 174 /mnt/bulleit/arnaud/Plate1/Merged/TRIA102_Gc_Plate~ -0.0102 -4.56e-3
## 175 /mnt/bulleit/arnaud/Plate7_9/TRIA665_Gc_Plate09_F0~ -0.0110 -4.55e-3
## 176 /mnt/bulleit/arnaud/Plate2_6/ss262_Gc_Plate02_F02.~ -0.00985 -4.50e-3
## 177 /mnt/bulleit/arnaud/Plate2_6/TRIA924_Gc_Plate04_E0~ -0.00929 -4.49e-3
## 178 /mnt/bulleit/arnaud/Plate2_6/TRIA127_Gc_Plate02_E0~ -0.00962 -4.48e-3
## 179 /mnt/bulleit/arnaud/Plate2_6/TRIA175_Gc_Plate02_D1~ -0.0105 -4.44e-3
## 180 /mnt/bulleit/arnaud/Plate2_6/TRIA169_Gc_Plate02_F1~ -0.0105 -4.44e-3
## 181 /mnt/bulleit/arnaud/Plate2_6/TRIA91_Gc_Plate02_H07~ -0.0106 -4.40e-3
## 182 /mnt/bulleit/arnaud/Plate2_6/TRIA104_Gc_Plate02_D0~ -0.0105 -4.39e-3
## 183 /mnt/bulleit/arnaud/Plate7_9/TRIA92_Gc_Plate07_C07~ -0.0105 -4.39e-3
## 184 /mnt/bulleit/arnaud/Plate7_9/ss58_Gc_Plate07_C01.s~ -0.0105 -4.36e-3
## 185 /mnt/bulleit/arnaud/Plate2_6/TRIA872_Gc_Plate03_F1~ -0.0110 -4.36e-3
## 186 /mnt/bulleit/arnaud/Plate1/Merged/TRIA97_Gc_Plate0~ -0.00910 -4.34e-3
## 187 /mnt/bulleit/arnaud/merged_bam/TRIA111_Gc_merged_s~ -0.00910 -4.34e-3
## 188 /mnt/bulleit/arnaud/Plate7_9/TRIA294_Gc_Plate07_A0~ -0.00903 -4.26e-3
## 189 /mnt/bulleit/arnaud/Plate2_6/TRIA181_Gc_Plate02_H1~ -0.0118 -4.25e-3
## 190 /mnt/bulleit/arnaud/Plate2_6/TRIA95_Gc_Plate02_A08~ -0.00782 -4.24e-3
## 191 /mnt/bulleit/arnaud/Plate7_9/TRIA820_Gc_Plate09_D0~ -0.0108 -4.23e-3
## 192 /mnt/bulleit/arnaud/Plate2_6/TRIA515_Gc_Plate06_F0~ -0.0106 -4.20e-3
## 193 /mnt/bulleit/arnaud/Plate2_6/TRIA183_Gc_Plate03_B0~ -0.0109 -4.19e-3
## 194 /mnt/bulleit/arnaud/Plate2_6/ss479_Gc_Plate02_B05.~ -0.0120 -4.18e-3
## 195 /mnt/bulleit/arnaud/Plate7_9/ss402_Gc_Plate07_A05.~ -0.0113 -4.16e-3
## 196 /mnt/bulleit/arnaud/Plate2_6/TRIA865_Gc_Plate03_C1~ -0.00934 -4.16e-3
## 197 /mnt/bulleit/arnaud/Plate2_6/TRIA510_Gc_Plate03_D0~ -0.0106 -4.13e-3
## 198 /mnt/bulleit/arnaud/Plate2_6/TRIA184_Gc_Plate03_C0~ -0.00911 -4.13e-3
## 199 /mnt/bulleit/arnaud/Plate2_6/TRIA868_Gc_Plate03_E1~ -0.0104 -4.13e-3
## 200 /mnt/bulleit/arnaud/Plate2_6/TRIA864_Gc_Plate03_B1~ -0.00921 -4.08e-3
## 201 /mnt/bulleit/arnaud/Plate2_6/TRIA386_Gc_Plate03_E0~ -0.00918 -4.07e-3
## 202 /mnt/bulleit/arnaud/Plate2_6/TRIA137_Gc_Plate02_C1~ -0.00931 -4.03e-3
## 203 /mnt/bulleit/arnaud/Plate2_6/TRIA279_Gc_Plate03_G0~ -0.0101 -4.02e-3
## 204 /mnt/bulleit/arnaud/Plate2_6/TRIA276_Gc_Plate03_E0~ -0.0101 -4.02e-3
## 205 /mnt/bulleit/arnaud/Plate2_6/TRIA108_Gc_Plate02_E0~ -0.0115 -4.01e-3
## 206 /mnt/bulleit/arnaud/Plate2_6/ss378_Gc_Plate02_B03.~ -0.0115 -4.00e-3
## 207 /mnt/bulleit/arnaud/Plate2_6/ss496_Gc_Plate02_D05.~ -0.0102 -3.89e-3
## 208 /mnt/bulleit/arnaud/Plate2_6/TRIA291_Gc_Plate03_B0~ -0.00817 -3.84e-3
## 209 /mnt/bulleit/arnaud/Plate2_6/ss205_Gc_Plate02_G01.~ -0.0101 -3.78e-3
## 210 /mnt/bulleit/arnaud/Plate2_6/ss258_Gc_Plate02_E02.~ -0.00823 -3.78e-3
## 211 /mnt/bulleit/arnaud/Plate2_6/TRIA141_Gc_Plate02_F1~ -0.00868 -3.74e-3
## 212 /mnt/bulleit/arnaud/Plate2_6/ss217_Gc_Plate02_A02.~ -0.0119 -3.74e-3
## 213 /mnt/bulleit/arnaud/Plate2_6/ss228_Gc_Plate02_C02.~ -0.0119 -3.73e-3
## 214 /mnt/bulleit/arnaud/Plate2_6/TRIA778_Gc_Plate03_C1~ -0.0107 -3.72e-3
## 215 /mnt/bulleit/arnaud/Plate2_6/TRIA439_Gc_Plate03_F0~ -0.00966 -3.72e-3
## 216 /mnt/bulleit/arnaud/Plate2_6/TRIA20_Gc_Plate02_H05~ -0.00950 -3.62e-3
## 217 /mnt/bulleit/arnaud/Plate2_6/TRIA80_Gc_Plate02_B07~ -0.00886 -3.59e-3
## 218 /mnt/bulleit/arnaud/Plate1/Merged/ss295_Gc_Plate01~ -0.00948 -3.51e-3
## 219 /mnt/bulleit/arnaud/Plate2_6/TRIA120_Gc_Plate06_B0~ -0.0105 -3.42e-3
## 220 /mnt/bulleit/arnaud/Plate2_6/TRIA300_Gc_Plate03_E0~ -0.0121 -3.35e-3
## 221 /mnt/bulleit/arnaud/Plate2_6/ss518_Gc_Plate06_C01.~ -0.00953 -3.33e-3
## 222 /mnt/bulleit/arnaud/Plate2_6/TRIA950_Gc_Plate04_C0~ -0.0106 -3.30e-3
## 223 /mnt/bulleit/arnaud/merged_bam/TRIA12_Gc_merged_so~ -0.0131 -3.30e-3
## 224 /mnt/bulleit/arnaud/Plate2_6/ss361_Gc_Plate02_A03.~ -0.00917 -3.27e-3
## 225 /mnt/bulleit/arnaud/Plate7_9/ss482_Gc_Plate07_F06.~ -0.0117 -3.17e-3
## 226 /mnt/bulleit/arnaud/Plate7_9/ss478_Gc_Plate07_D06.~ -0.00961 -3.13e-3
## 227 /mnt/bulleit/arnaud/Plate7_9/TRIA714_Gc_Plate09_D0~ -0.00903 -2.96e-3
## 228 /mnt/bulleit/arnaud/Plate2_6/TRIA170_Gc_Plate02_G1~ -0.00839 -2.89e-3
## 229 /mnt/bulleit/arnaud/Plate2_6/TRIA269_Gc_Plate03_H0~ -0.00899 -2.86e-3
## 230 /mnt/bulleit/arnaud/Plate2_6/ss169_Gc_Plate02_D01.~ -0.0119 -2.79e-3
## 231 /mnt/bulleit/arnaud/Plate2_6/ss389_Gc_Plate02_F03.~ -0.0121 -2.79e-3
## 232 /mnt/bulleit/arnaud/Plate2_6/ss500_Gc_Plate02_F05.~ -0.00848 -2.77e-3
## 233 /mnt/bulleit/arnaud/Plate2_6/TRIA887_Gc_Plate04_B0~ -0.00962 -2.77e-3
## 234 /mnt/bulleit/arnaud/Plate2_6/TRIA941_Gc_Plate04_F0~ -0.00740 -2.61e-3
## 235 /mnt/bulleit/arnaud/Plate2_6/TRIA843_Gc_Plate03_A1~ -0.00951 -2.56e-3
## 236 /mnt/bulleit/arnaud/Plate2_6/ss226_Gc_Plate02_B02.~ -0.00995 -2.36e-3
## 237 /mnt/bulleit/arnaud/Plate2_6/ss480_Gc_Plate02_C05.~ -0.00957 -2.30e-3
## 238 /mnt/bulleit/arnaud/Plate7_9/TRIA379_Gc_Plate07_E0~ -0.00818 -2.25e-3
## 239 /mnt/bulleit/arnaud/Plate2_6/TRIA830_Gc_Plate03_F1~ -0.00935 -2.09e-3
## 240 /mnt/bulleit/arnaud/Plate7_9/TRIA511_Gc_Plate07_E1~ -0.0103 -1.98e-3
## 241 /mnt/bulleit/arnaud/Plate2_6/TRIA908_Gc_Plate04_C0~ -0.00717 -1.75e-3
## 242 /mnt/bulleit/arnaud/Plate2_6/TRIA480_Gc_Plate03_H0~ -0.0105 -1.74e-3
## 243 /mnt/bulleit/arnaud/Plate7_9/ss257_Gc_Plate07_G03.~ -0.00779 -1.54e-3
## 244 /mnt/bulleit/arnaud/Plate2_6/TRIA115_Gc_Plate02_A0~ -0.00780 -4.15e-4
## 245 /mnt/bulleit/arnaud/Plate7_9/TRIA121_Gc_Plate07_E0~ -0.00775 -3.93e-4
## 246 /mnt/bulleit/arnaud/Plate2_6/TRIA588_Gc_Plate03_A0~ -0.00863 1.99e-3
## 247 /mnt/bulleit/arnaud/Plate2_6/TRIA587_Gc_Plate03_H0~ -0.00867 2.14e-3
## 248 /mnt/bulleit/arnaud/Plate2_6/TRIA610_Gc_Plate03_C0~ -0.00676 2.61e-3
## 249 /mnt/bulleit/arnaud/Plate2_6/TRIA602_Gc_Plate03_B0~ -0.00531 4.42e-3
## 250 /mnt/bulleit/arnaud/Plate7_9/TRIA612_Gc_Plate07_C1~ -0.000886 5.48e-3
## 251 /mnt/bulleit/arnaud/Plate2_6/TRIA986_Gc_Plate04_D0~ -0.00190 7.57e-3
## 252 /mnt/bulleit/arnaud/Plate2_6/TRIA990_Gc_Plate04_E0~ -0.00157 7.70e-3
## 253 /mnt/bulleit/arnaud/Plate2_6/TRIA650_Gc_Plate03_G0~ 0.00404 9.24e-3
## 254 /mnt/bulleit/arnaud/Plate2_6/TRIA984_Gc_Plate04_C0~ 0.00334 9.72e-3
## 255 /mnt/bulleit/arnaud/Plate2_6/TRIA878_Gc_Plate04_A0~ 0.00309 1.25e-2
## 256 /mnt/bulleit/arnaud/Plate2_6/TRIA877_Gc_Plate03_H1~ 0.00654 1.40e-2
## 257 /mnt/bulleit/arnaud/Plate2_6/TRIA467_Gc_Plate03_G0~ 0.0178 2.04e-2## # A tibble: 7 x 3
## sample.id EV1 EV2
## <chr> <dbl> <dbl>
## 1 /mnt/bulleit/arnaud/Plate7_9/TRIA821_Gc_Plate09_E07.sorted.~ 0.182 0.282
## 2 /mnt/bulleit/arnaud/Plate2_6/TRIA809_Gc_Plate03_D11.sorted.~ 0.192 0.294
## 3 /mnt/bulleit/arnaud/Plate2_6/TRIA177_Gc_Plate06_G02.sorted.~ 0.202 0.302
## 4 /mnt/bulleit/arnaud/Plate2_6/TRIA7_Gc_Plate06_D01.sorted.bam 0.215 0.311
## 5 /mnt/bulleit/arnaud/Plate2_6/TRIA75_Gc_Plate02_G06.sorted.b~ 0.217 0.320
## 6 /mnt/bulleit/arnaud/Plate2_6/TRIA799_Gc_Plate03_A11.sorted.~ 0.218 0.321
## 7 /mnt/bulleit/arnaud/Plate1/Merged/TRIA66_Gc_Plate01_G04.sor~ 0.219 0.332