Test Page
Zachary Chen
2022-11-28
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getwd()## [1] "C:/Users/Zachy/OneDrive/Desktop/compbioFall22"setwd("C:/Users/Zachy/OneDrive/Desktop/compbioFall22")
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
## ***** ***** ***** *****list.files()## [1] "21.16015248-16255248.ALL.chr21_GRCh38.genotypes.20170504.vcf.gz"
## [2] "all_loci.vcf"
## [3] "my_snp.vcf.gz"
## [4] "rsconnect"
## [5] "Screenshot 2022-11-28 082623.jpg"
## [6] "TestPage.Rmd"
## [7] "transpose_VCF_data.html"
## [8] "transpose_VCF_data.Rmd"
## [9] "walsh2017morphology.csv"
## [10] "working_directory_practice.html"
## [11] "working_directory_practice.Rmd"my_snps<- vcfR::read.vcfR("21.16015248-16255248.ALL.chr21_GRCh38.genotypes.20170504.vcf.gz")## Scanning file to determine attributes.
## File attributes:
## meta lines: 130
## header_line: 131
## variant count: 563
## column count: 2513
##
Meta line 130 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 563
## Character matrix gt cols: 2513
## skip: 0
## nrows: 563
## row_num: 0
##
Processed variant: 563
## All variants processedhead(my_snps)## [1] "***** Object of class 'vcfR' *****"
## [1] "***** Meta section *****"
## [1] "##fileformat=VCFv4.1"
## [1] "##FILTER=<ID=PASS,Description=\"All filters passed\">"
## [1] "##fileDate=20150218"
## [1] "##reference=ftp://ftp.1000genomes.ebi.ac.uk//vol1/ftp/technical/refe [Truncated]"
## [1] "##source=1000GenomesPhase3Pipeline"
## [1] "##contig=<ID=1,assembly=b37,length=249250621>"
## [1] "First 6 rows."
## [1]
## [1] "***** Fixed section *****"
## CHROM POS ID REF ALT QUAL FILTER
## [1,] "21" "16015384" "rs541919137" "A" "C" "100" "PASS"
## [2,] "21" "16015462" "rs561279655" "G" "T" "100" "PASS"
## [3,] "21" "16015472" "rs139596006" "G" "A" "100" "PASS"
## [4,] "21" "16015510" "rs34840784" "C" "T" "100" "PASS"
## [5,] "21" "16015511" "rs182398501" "G" "A" "100" "PASS"
## [6,] "21" "16015553" "rs75781173" "T" "C" "100" "PASS"
## [1]
## [1] "***** Genotype section *****"
## FORMAT HG00096 HG00097 HG00099 HG00100 HG00101
## [1,] "GT" "0|0" "0|0" "0|0" "0|0" "0|0"
## [2,] "GT" "0|0" "0|0" "0|0" "0|0" "0|0"
## [3,] "GT" "0|0" "1|1" "0|0" "0|0" "0|0"
## [4,] "GT" "0|0" "0|0" "0|0" "0|0" "0|0"
## [5,] "GT" "0|0" "0|0" "0|0" "0|0" "0|0"
## [6,] "GT" "1|1" "1|1" "1|1" "0|1" "0|1"
## [1] "First 6 columns only."
## [1]
## [1] "Unique GT formats:"
## [1] "GT"
## [1]summary(my_snps)## Length Class Mode
## 1 vcfR S4my_snps_num <- vcfR::extract.gt(my_snps, # TODO
element = "GT",
IDtoRowNames = F,
as.numeric = T,
convertNA = T)
my_snps_num_t<-t(my_snps_num)
no_NA<- na.omit(my_snps_num_t)
dim(my_snps_num_t)## [1] 2504 563no_NA## [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
## HG00096 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00097 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00099 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00100 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00101 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00102 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00103 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00105 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00106 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00107 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00108 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00109 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00110 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00111 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00112 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00113 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00114 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00115 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00116 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00117 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00118 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00119 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00120 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00121 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00122 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00123 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00125 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00126 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00127 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00128 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00129 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00130 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00131 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00132 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00133 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00136 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00137 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00138 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00139 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00140 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00141 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00142 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00143 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00145 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00146 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00148 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00149 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00150 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00151 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00154 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00155 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00157 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00158 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00159 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00160 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00171 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00173 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00174 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00176 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00177 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00178 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00179 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00180 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00181 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00182 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00183 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00185 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00186 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00187 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00188 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00189 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00190 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00231 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00232 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00233 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00234 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00235 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00236 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00237 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00238 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00239 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00240 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00242 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00243 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00244 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00245 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00246 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00250 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00251 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00252 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00253 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00254 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00255 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00256 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00257 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00258 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00259 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00260 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00261 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00262 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00263 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00264 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00265 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00266 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00267 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00268 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00269 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00271 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00272 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00273 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00274 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00275 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00276 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00277 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00278 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00280 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00281 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00282 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00284 0 0 0 0 0 1 1 1 1 0 0 1 0
## HG00285 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00288 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00290 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00304 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00306 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00308 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00309 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00310 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00311 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00313 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00315 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00318 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00319 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00320 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00321 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00323 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00324 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00325 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00326 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00327 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00328 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00329 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00330 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00331 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00332 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00334 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00335 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00336 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00337 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00338 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00339 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00341 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00342 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00343 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00344 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00345 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00346 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00349 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00350 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00351 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00353 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00355 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00356 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00357 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00358 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00360 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00361 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00362 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00364 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00365 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00366 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00367 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00368 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00369 0 0 0 0 0 0 0 0 0 0 0 0 0
## HG00371 0 0 1 0 0 1 0 1 1 0 0 1 0
## HG00372 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00373 0 0 0 0 0 1 0 1 1 0 0 1 0
## HG00375 0 0 0 0 0 1 0 1 1 0 0 1 0
## [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
## HG00096 0 0 0 0 1 0 0 0 1 0 0 0
## HG00097 0 0 0 0 1 0 0 0 1 0 0 0
## HG00099 0 0 0 0 1 0 0 0 1 0 0 0
## HG00100 0 0 0 0 0 0 0 0 0 0 0 0
## HG00101 0 0 0 0 0 0 0 0 0 0 0 0
## HG00102 0 0 0 0 1 0 0 0 1 0 0 0
## HG00103 0 0 0 0 1 0 0 0 1 0 0 0
## HG00105 0 0 0 0 1 0 0 0 1 0 0 0
## HG00106 0 0 0 0 1 0 0 0 1 0 0 0
## HG00107 0 0 0 0 1 0 0 0 1 0 0 0
## HG00108 0 0 0 0 1 0 0 0 1 0 0 0
## HG00109 0 0 0 0 1 0 0 0 1 0 0 0
## HG00110 0 0 0 0 1 0 0 0 1 0 0 0
## HG00111 0 0 0 0 1 0 0 0 1 0 0 0
## HG00112 0 0 0 0 1 0 0 0 1 0 0 0
## HG00113 0 0 0 0 1 0 0 0 1 0 0 0
## HG00114 0 0 0 0 1 0 0 0 1 0 0 0
## HG00115 0 0 0 0 1 0 0 0 1 0 0 0
## HG00116 0 0 0 0 0 0 0 0 0 0 0 0
## HG00117 0 0 0 0 1 0 0 0 1 0 0 0
## HG00118 0 0 0 0 1 0 0 0 1 0 0 0
## HG00119 0 0 0 0 0 0 0 0 0 0 0 0
## HG00120 0 0 0 0 0 0 0 0 0 0 0 0
## HG00121 0 0 0 0 1 0 0 0 1 0 0 0
## HG00122 0 0 0 0 0 0 0 0 0 0 0 0
## HG00123 0 0 0 0 0 0 0 0 0 0 0 0
## HG00125 0 0 0 0 1 0 0 0 1 0 0 0
## HG00126 0 0 0 0 1 0 0 0 1 0 0 0
## HG00127 0 0 0 0 0 0 0 0 0 0 0 0
## HG00128 0 0 0 0 1 0 0 0 1 0 0 0
## HG00129 0 0 0 0 1 0 0 0 1 0 0 0
## HG00130 0 0 0 0 1 0 0 0 1 0 0 0
## HG00131 0 0 0 0 1 0 0 0 1 0 0 0
## HG00132 0 0 0 0 0 0 0 0 0 0 0 0
## HG00133 0 0 0 0 1 0 0 0 1 0 0 0
## HG00136 0 0 0 0 1 0 0 0 1 0 0 0
## HG00137 0 0 0 0 1 0 0 0 1 0 0 0
## HG00138 0 0 0 0 1 0 0 0 1 0 0 0
## HG00139 0 0 0 0 1 0 0 0 1 0 0 0
## HG00140 0 0 0 0 1 0 0 0 1 0 0 0
## HG00141 0 0 0 0 1 0 0 0 1 0 0 0
## HG00142 0 0 0 0 1 0 0 0 1 0 0 0
## HG00143 0 0 0 0 1 0 0 0 1 0 0 0
## HG00145 0 0 0 0 1 0 0 0 1 0 0 0
## HG00146 0 0 0 0 1 0 0 0 1 0 0 0
## HG00148 0 0 0 0 1 0 0 0 1 0 0 0
## HG00149 0 0 0 0 1 0 0 0 1 0 0 0
## HG00150 0 0 0 0 1 0 0 0 1 0 0 0
## HG00151 0 0 0 0 1 0 0 0 1 0 0 0
## HG00154 0 0 0 0 1 0 0 0 1 0 0 0
## HG00155 0 0 0 0 0 0 0 0 0 0 0 0
## HG00157 0 0 0 0 0 0 0 0 0 0 0 0
## HG00158 0 0 0 0 1 0 0 0 1 0 0 0
## HG00159 0 0 0 0 0 0 0 0 0 0 0 0
## HG00160 0 0 0 0 1 0 0 0 1 0 0 0
## HG00171 0 0 0 0 1 0 0 0 1 0 0 0
## HG00173 0 0 0 0 1 0 0 0 1 0 0 0
## HG00174 0 0 0 0 1 0 0 0 1 0 0 0
## HG00176 0 0 0 0 1 0 0 0 1 0 0 0
## HG00177 0 0 0 0 0 0 0 0 0 0 0 0
## HG00178 0 0 0 0 1 0 0 0 1 0 0 0
## HG00179 0 0 0 0 1 0 0 0 1 0 0 0
## HG00180 0 0 0 0 0 0 0 0 0 0 0 0
## HG00181 0 0 0 0 0 0 0 0 0 0 0 0
## HG00182 0 0 0 0 1 0 0 0 1 0 0 0
## HG00183 0 0 0 0 1 0 0 0 1 0 0 0
## HG00185 0 0 0 0 0 0 0 0 0 0 0 0
## HG00186 0 0 0 0 1 0 0 0 1 0 0 0
## HG00187 0 0 0 0 1 0 0 0 1 0 0 0
## HG00188 0 0 0 0 1 0 0 0 1 0 0 0
## HG00189 0 0 0 0 1 0 0 0 1 0 0 0
## HG00190 0 0 0 0 1 0 0 0 1 0 0 0
## HG00231 0 0 0 0 1 0 0 0 1 0 0 0
## HG00232 0 0 0 0 1 0 0 0 1 0 0 0
## HG00233 0 0 0 0 1 0 0 0 1 0 0 0
## HG00234 0 0 0 0 1 0 0 0 1 0 0 0
## HG00235 0 0 0 0 0 0 0 0 0 0 0 0
## HG00236 0 0 0 0 1 0 0 0 1 0 0 0
## HG00237 0 0 0 0 1 0 0 0 1 0 0 0
## HG00238 0 0 0 0 1 0 0 0 1 0 0 0
## HG00239 0 0 0 0 1 0 0 0 1 0 0 0
## HG00240 0 0 0 0 1 0 0 0 1 0 0 0
## HG00242 0 0 0 0 1 0 0 0 1 0 0 0
## HG00243 0 0 0 0 0 0 0 0 0 0 0 0
## HG00244 0 0 0 0 0 0 0 0 0 0 0 0
## HG00245 0 0 0 0 0 0 0 0 0 0 0 0
## HG00246 0 0 0 0 1 0 0 0 1 0 0 0
## HG00250 0 0 0 0 1 0 0 0 1 0 0 0
## HG00251 0 0 0 0 1 0 0 0 1 0 0 0
## HG00252 0 0 0 0 1 0 0 0 1 0 0 0
## HG00253 0 0 0 0 1 0 0 0 1 0 0 0
## HG00254 0 0 0 0 1 0 0 0 1 0 0 0
## HG00255 0 0 0 0 1 0 0 0 1 0 0 0
## HG00256 0 0 0 0 1 0 0 0 1 0 0 0
## HG00257 0 0 0 0 1 0 0 0 1 0 0 0
## HG00258 0 0 0 0 1 0 0 0 1 0 0 0
## HG00259 0 0 0 0 1 0 0 0 1 0 0 0
## HG00260 0 0 0 0 0 0 0 0 0 0 0 0
## HG00261 0 0 0 0 1 0 0 0 1 0 0 0
## HG00262 0 0 0 0 1 0 0 0 1 0 0 0
## HG00263 0 0 0 0 1 0 0 0 1 0 0 0
## HG00264 0 0 0 0 0 0 0 0 0 0 0 0
## HG00265 0 0 0 0 0 0 0 0 0 0 0 0
## HG00266 0 0 0 0 0 0 0 0 0 0 0 0
## HG00267 0 0 0 0 1 0 0 0 1 0 0 0
## HG00268 0 0 0 0 1 0 0 0 1 0 0 0
## HG00269 0 0 0 0 1 0 0 0 1 0 0 0
## HG00271 0 0 0 0 1 0 0 0 1 0 0 0
## HG00272 0 0 0 0 1 0 0 0 1 0 0 0
## HG00273 0 0 0 0 1 0 0 0 1 0 0 0
## HG00274 0 0 0 0 1 0 0 0 1 0 0 0
## HG00275 0 0 0 0 1 0 0 0 1 0 0 0
## HG00276 0 0 0 0 1 0 0 0 1 0 0 0
## HG00277 0 0 0 0 1 0 0 0 1 0 0 0
## HG00278 0 0 0 0 1 0 0 0 1 0 0 0
## HG00280 0 0 0 0 0 0 0 0 0 0 0 0
## HG00281 0 0 0 0 1 0 0 0 1 0 0 0
## HG00282 0 0 0 0 1 0 0 0 1 0 0 0
## HG00284 0 0 0 0 1 0 0 0 1 0 0 0
## HG00285 0 0 0 0 1 0 0 0 1 0 0 0
## HG00288 0 0 0 0 1 0 0 0 1 0 0 0
## HG00290 0 0 0 0 1 0 0 0 1 0 0 0
## HG00304 0 0 0 0 1 0 0 0 1 0 0 0
## HG00306 0 0 0 0 1 0 0 0 1 0 0 0
## HG00308 0 0 0 0 1 0 0 0 1 0 0 0
## HG00309 0 0 0 0 1 0 0 0 1 0 0 0
## HG00310 0 0 0 0 0 0 0 0 0 0 0 0
## HG00311 0 0 0 0 1 0 0 0 1 0 0 0
## HG00313 0 0 0 0 0 0 0 0 0 0 0 0
## HG00315 0 0 0 0 0 0 0 0 0 0 0 0
## HG00318 0 0 0 0 0 0 0 0 0 0 0 0
## HG00319 0 0 0 0 1 0 0 0 1 0 0 0
## HG00320 0 0 0 0 1 0 0 0 1 0 0 0
## HG00321 0 0 0 0 0 0 0 0 0 0 0 0
## HG00323 0 0 0 0 1 0 0 0 1 0 0 0
## HG00324 0 0 0 0 1 0 0 0 1 0 0 0
## HG00325 0 0 0 0 1 0 0 0 1 0 0 0
## HG00326 0 0 0 0 1 0 0 0 1 0 0 0
## HG00327 0 0 0 0 1 0 0 0 1 0 0 0
## HG00328 0 0 0 0 1 0 0 0 1 0 0 0
## HG00329 0 0 0 0 0 0 0 0 0 0 0 0
## HG00330 0 0 0 0 1 0 0 0 1 0 0 0
## HG00331 0 0 0 0 0 0 0 0 0 0 0 0
## HG00332 0 0 0 0 1 0 0 0 1 0 0 0
## HG00334 0 0 0 0 0 0 0 0 0 0 0 0
## HG00335 0 0 0 0 1 0 0 0 1 0 0 0
## HG00336 0 0 0 0 1 0 0 0 1 0 0 0
## HG00337 0 0 0 0 1 0 0 0 1 0 0 0
## HG00338 0 0 0 0 1 0 0 0 1 0 0 0
## HG00339 0 0 0 0 1 0 0 0 1 0 0 0
## HG00341 0 0 0 0 1 0 0 0 1 0 0 0
## HG00342 0 0 0 0 1 0 0 0 1 0 0 0
## HG00343 0 0 0 0 0 0 0 0 0 0 0 0
## HG00344 0 0 0 0 1 0 0 0 1 0 0 0
## HG00345 0 0 0 0 1 0 0 0 1 0 0 0
## HG00346 0 0 0 0 1 0 0 0 1 0 0 0
## HG00349 0 0 0 0 1 0 0 0 1 0 0 0
## HG00350 0 0 0 0 0 0 0 0 0 0 0 0
## HG00351 0 0 0 0 1 0 0 0 1 0 0 0
## HG00353 0 0 0 0 1 0 0 0 1 0 0 0
## HG00355 0 0 0 0 1 0 0 0 1 0 0 0
## HG00356 0 0 0 0 1 0 0 0 1 0 0 0
## HG00357 0 0 0 0 1 0 0 0 1 0 0 0
## HG00358 0 0 0 0 0 0 0 0 0 0 0 0
## HG00360 0 0 0 0 1 0 0 0 1 0 0 0
## HG00361 0 0 0 0 1 0 0 0 1 0 0 0
## HG00362 0 0 0 0 1 0 0 0 1 0 0 0
## HG00364 0 0 0 0 1 0 0 0 1 0 0 0
## HG00365 0 0 0 0 0 0 0 0 0 0 0 0
## HG00366 0 0 0 0 1 0 0 0 1 0 0 0
## HG00367 0 0 0 0 1 0 0 0 1 0 0 0
## HG00368 0 0 0 0 0 0 0 0 0 0 0 0
## HG00369 0 0 0 0 0 0 0 0 0 0 0 0
## HG00371 0 0 0 0 1 0 0 0 1 0 0 0
## HG00372 0 0 0 0 1 0 0 0 1 0 0 0
## HG00373 0 0 0 0 1 0 0 0 1 0 0 0
## HG00375 0 0 0 0 1 0 0 0 1 0 0 0
## [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37]
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## [,38] [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48] [,49]
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## [,148] [,149] [,150] [,151] [,152] [,153] [,154] [,155] [,156] [,157]
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## HG00190 0 0 0 0 0 0 0 0 0 0
## HG00231 0 0 0 0 0 0 0 0 0 0
## HG00232 0 0 0 0 0 0 0 0 0 0
## HG00233 0 0 0 0 0 0 0 0 0 0
## HG00234 0 0 0 0 0 0 0 0 0 0
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## HG00269 0 0 0 0 0 0 0 0 0 0
## HG00271 0 0 0 0 0 0 0 0 0 0
## HG00272 0 0 0 0 0 0 0 0 0 0
## HG00273 0 0 0 0 0 0 0 0 0 0
## HG00274 0 0 0 0 0 0 0 0 0 0
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## HG00277 0 0 0 0 0 0 0 0 0 0
## HG00278 0 0 0 0 0 0 0 0 0 0
## HG00280 0 0 0 0 0 0 0 0 0 0
## HG00281 0 0 0 0 0 0 0 0 0 0
## HG00282 0 0 0 0 0 0 0 0 0 0
## HG00284 0 0 0 0 0 0 0 0 0 0
## HG00285 0 0 0 0 0 0 0 0 0 0
## HG00288 0 0 0 0 0 0 0 0 0 0
## HG00290 0 0 0 0 0 0 0 0 0 0
## HG00304 0 0 0 0 0 0 0 0 0 0
## HG00306 0 0 0 0 0 0 0 0 0 0
## HG00308 0 0 0 0 0 0 0 0 0 0
## HG00309 0 0 0 0 0 0 0 0 0 0
## HG00310 0 0 0 0 0 0 0 0 0 0
## HG00311 0 0 0 0 0 0 0 0 0 0
## HG00313 0 0 0 0 0 0 0 0 0 0
## HG00315 0 0 0 0 0 0 0 0 0 0
## HG00318 0 0 0 0 0 0 0 0 0 0
## HG00319 0 0 0 0 0 0 0 0 0 0
## HG00320 0 0 0 0 0 0 0 0 0 0
## HG00321 0 0 0 0 0 0 0 0 0 0
## HG00323 0 0 0 0 0 0 0 0 0 0
## HG00324 0 0 0 0 0 0 0 0 0 0
## HG00325 0 0 0 0 0 0 0 0 0 0
## HG00326 0 0 0 0 0 0 0 0 0 0
## HG00327 0 0 0 0 0 0 0 0 0 0
## HG00328 0 0 0 0 0 0 0 0 0 0
## HG00329 0 0 0 0 0 0 0 0 0 0
## HG00330 0 0 0 0 0 0 0 0 0 0
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## HG00339 0 0 0 0 0 0 0 0 0 0
## HG00341 0 0 0 0 0 0 0 0 0 0
## HG00342 0 0 0 0 0 0 0 0 0 0
## HG00343 0 0 0 0 0 0 0 0 0 0
## HG00344 0 0 0 0 0 0 0 0 0 0
## HG00345 0 0 0 0 0 0 0 0 0 0
## HG00346 0 0 0 0 0 0 0 0 0 0
## HG00349 0 0 0 0 0 0 0 0 0 0
## HG00350 0 0 0 0 0 0 0 0 0 0
## HG00351 0 0 0 0 0 0 0 0 0 0
## HG00353 0 0 0 0 0 0 0 0 0 0
## HG00355 0 0 0 0 0 0 0 0 0 0
## HG00356 0 0 0 0 0 0 0 0 0 0
## HG00357 0 0 0 0 0 0 0 0 0 0
## HG00358 0 0 0 0 0 0 0 0 0 0
## HG00360 0 0 0 0 0 0 0 0 0 0
## HG00361 0 0 0 0 0 0 0 0 0 0
## HG00362 0 0 0 0 0 0 0 0 0 0
## HG00364 0 0 0 0 0 0 0 0 0 0
## HG00365 0 0 0 0 0 0 0 0 0 0
## HG00366 0 0 0 0 0 0 0 0 1 0
## HG00367 0 0 0 0 0 0 0 0 0 0
## HG00368 0 0 0 0 0 0 0 0 0 0
## HG00369 0 0 0 0 0 0 0 0 0 0
## HG00371 0 0 0 0 0 0 0 0 0 0
## HG00372 0 0 0 0 0 0 0 0 0 0
## HG00373 0 0 0 0 0 0 0 0 0 0
## HG00375 0 0 0 0 0 0 0 0 0 0
## [,178] [,179] [,180] [,181] [,182] [,183] [,184] [,185] [,186] [,187]
## HG00096 0 0 0 0 0 0 0 0 0 0
## HG00097 0 0 0 0 0 0 0 0 0 0
## HG00099 0 0 0 0 0 0 0 0 0 0
## HG00100 0 0 0 0 0 0 0 0 0 0
## HG00101 0 0 0 0 0 0 0 0 0 0
## HG00102 0 0 0 0 0 0 0 0 0 0
## HG00103 0 0 0 0 0 0 0 0 0 0
## HG00105 0 0 0 0 0 0 0 0 0 0
## HG00106 0 0 0 0 0 0 0 0 0 0
## HG00107 0 0 0 0 0 0 0 0 0 0
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## HG00116 0 0 0 0 0 0 0 0 0 0
## HG00117 0 0 0 0 0 0 0 0 0 0
## HG00118 0 0 0 0 0 0 0 0 0 0
## HG00119 0 0 0 0 0 0 0 0 0 0
## HG00120 0 0 0 0 0 0 0 0 0 0
## HG00121 0 0 0 0 0 0 0 0 0 0
## HG00122 0 0 0 0 0 0 0 0 0 0
## HG00123 0 0 0 0 0 0 0 0 0 0
## HG00125 0 0 0 0 0 0 0 0 0 0
## HG00126 0 0 0 0 0 0 0 0 0 0
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## HG00128 0 0 0 0 0 0 0 0 0 0
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## HG00130 0 0 0 0 0 0 0 0 0 0
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## HG00136 0 0 0 0 0 0 0 0 0 0
## HG00137 0 0 0 0 0 0 0 0 0 0
## HG00138 0 0 0 0 0 0 0 0 0 0
## HG00139 0 0 0 0 0 0 0 0 0 0
## HG00140 0 0 0 0 0 0 0 0 0 0
## HG00141 0 0 0 0 0 0 0 0 0 0
## HG00142 0 0 0 0 0 0 0 0 0 0
## HG00143 0 0 0 0 0 0 0 0 0 0
## HG00145 0 0 0 0 0 0 0 0 0 0
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## HG00157 0 0 0 0 0 0 0 0 0 0
## HG00158 0 0 0 0 0 0 0 0 0 0
## HG00159 0 0 0 0 0 0 0 0 0 0
## HG00160 0 0 0 0 0 0 0 0 0 0
## HG00171 0 0 0 0 0 0 0 0 0 0
## HG00173 0 0 0 0 0 0 0 0 0 0
## HG00174 0 0 0 0 0 0 0 0 0 0
## HG00176 0 0 0 0 0 0 0 0 0 0
## HG00177 0 0 0 0 0 0 0 0 0 0
## HG00178 0 0 0 0 0 0 0 0 0 0
## HG00179 0 0 0 0 0 0 0 0 0 0
## HG00180 0 0 0 0 0 0 0 0 0 0
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## HG00242 0 0 0 0 0 0 0 0 0 0
## HG00243 0 0 0 0 0 0 0 1 0 0
## HG00244 0 0 0 0 0 0 0 0 0 0
## HG00245 0 0 0 0 0 0 0 0 0 0
## HG00246 0 0 0 0 0 0 0 0 0 0
## HG00250 0 0 0 0 0 0 0 0 0 0
## HG00251 0 0 0 0 0 0 0 0 0 0
## HG00252 0 0 0 0 0 0 0 0 0 0
## HG00253 0 0 0 0 0 0 0 0 0 0
## HG00254 0 0 0 0 0 0 0 0 0 0
## HG00255 0 0 0 0 0 0 0 0 0 0
## HG00256 0 0 0 0 0 0 0 0 0 0
## HG00257 0 0 0 0 0 0 0 0 0 0
## HG00258 0 0 0 0 0 0 0 0 0 0
## HG00259 0 0 0 0 0 0 0 0 0 0
## HG00260 0 0 0 0 0 0 0 0 0 0
## HG00261 0 0 0 0 0 0 0 0 0 0
## HG00262 0 0 0 0 0 0 0 0 0 0
## HG00263 0 0 0 0 0 0 0 0 0 0
## HG00264 0 0 0 0 0 0 0 0 0 0
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## HG00288 0 0 0 0 0 0 0 0 0 0
## HG00290 0 0 0 0 0 0 0 0 0 0
## HG00304 0 0 0 0 0 0 0 0 0 0
## HG00306 0 0 0 0 0 0 0 0 0 0
## HG00308 0 0 0 0 0 0 0 0 0 0
## HG00309 0 0 0 0 0 0 0 0 0 0
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## HG00318 0 0 0 0 0 0 0 0 0 0
## HG00319 0 0 0 0 0 0 0 0 0 0
## HG00320 0 0 0 0 0 0 0 0 0 0
## HG00321 0 0 0 0 0 0 0 0 0 0
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## HG00344 0 0 0 0 0 0 0 0 0 0
## HG00345 0 0 0 0 0 0 0 0 0 0
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## HG00353 0 0 0 0 0 0 0 0 0 0
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## HG00356 0 0 0 0 0 0 0 0 0 0
## HG00357 0 0 0 0 0 0 0 0 0 0
## HG00358 0 0 0 0 0 0 0 0 0 0
## HG00360 0 0 0 0 0 0 0 0 0 0
## HG00361 0 0 0 0 0 0 0 0 0 0
## HG00362 0 0 0 0 0 0 0 0 0 0
## HG00364 0 0 0 0 0 0 0 0 0 0
## HG00365 0 0 0 0 0 0 0 0 0 0
## HG00366 0 0 0 0 0 0 0 0 0 0
## HG00367 0 0 0 0 0 0 0 0 0 0
## HG00368 0 0 0 0 0 0 0 0 0 0
## HG00369 0 0 0 0 0 0 0 0 0 0
## HG00371 0 0 0 0 0 0 0 0 0 0
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## HG00375 0 0 0 0 0 0 0 0 0 0
## [,188] [,189] [,190] [,191] [,192] [,193] [,194] [,195] [,196] [,197]
## HG00096 1 0 0 0 0 0 0 0 0 0
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## HG00102 1 0 0 0 0 0 0 0 0 0
## HG00103 1 0 0 0 0 0 0 0 0 0
## HG00105 1 0 0 0 0 0 0 0 0 0
## HG00106 1 0 0 0 0 0 0 0 0 0
## HG00107 1 0 0 1 0 0 0 0 0 0
## HG00108 1 0 0 0 0 0 0 0 0 0
## HG00109 1 0 0 0 0 0 0 0 0 0
## HG00110 1 0 0 0 0 0 0 0 0 0
## HG00111 1 0 0 0 0 0 0 0 0 0
## HG00112 1 0 0 0 0 0 0 0 0 0
## HG00113 1 0 0 0 0 0 0 0 0 0
## HG00114 1 0 0 0 0 0 0 0 0 0
## HG00115 1 0 0 0 0 0 0 0 0 0
## HG00116 0 0 0 0 0 0 0 0 0 0
## HG00117 1 0 0 0 0 0 0 0 0 0
## HG00118 1 0 0 0 0 0 0 0 0 0
## HG00119 0 0 0 0 0 0 0 0 0 0
## HG00120 0 0 0 0 0 0 0 0 0 0
## HG00121 1 0 0 0 0 0 0 0 0 0
## HG00122 0 0 0 0 0 0 0 0 0 0
## HG00123 0 0 0 0 0 0 0 0 0 0
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## HG00139 1 0 0 0 0 0 0 0 0 0
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## HG00143 1 0 0 0 0 0 0 0 0 0
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## HG00155 0 0 0 0 0 0 0 0 0 0
## HG00157 0 0 0 0 0 0 0 0 0 0
## HG00158 1 0 0 0 0 0 0 0 0 0
## HG00159 0 0 0 0 0 0 0 0 0 0
## HG00160 1 0 0 0 0 0 0 0 0 0
## HG00171 1 0 0 0 0 0 0 0 0 0
## HG00173 1 0 0 0 0 0 0 0 0 0
## HG00174 1 0 0 0 0 0 0 0 0 0
## HG00176 1 0 0 0 0 0 0 0 0 0
## HG00177 0 0 0 0 0 0 0 0 0 0
## HG00178 1 0 0 0 0 0 0 0 0 0
## HG00179 1 0 0 0 0 0 0 0 0 0
## HG00180 0 0 0 0 0 0 0 0 0 0
## HG00181 0 0 0 0 0 0 0 0 0 0
## HG00182 1 0 0 0 0 0 0 0 0 0
## HG00183 1 0 0 0 0 0 0 0 0 0
## HG00185 0 0 0 0 0 0 0 0 0 0
## HG00186 1 0 0 0 0 0 0 0 0 0
## HG00187 1 0 0 0 0 0 0 0 0 0
## HG00188 1 0 0 0 0 0 0 0 0 0
## HG00189 1 0 0 0 0 0 0 0 0 0
## HG00190 1 0 0 0 0 0 0 0 0 0
## HG00231 1 0 0 0 0 0 0 0 0 0
## HG00232 1 0 0 0 0 0 0 0 0 0
## HG00233 1 0 0 0 0 0 0 0 0 0
## HG00234 1 0 0 0 0 0 0 0 0 0
## HG00235 0 0 0 0 0 0 0 0 0 0
## HG00236 1 0 0 0 0 0 0 0 0 0
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## HG00242 1 0 0 0 0 0 0 0 0 0
## HG00243 0 0 0 0 0 0 0 0 0 0
## HG00244 0 0 0 0 0 0 0 0 0 0
## HG00245 0 0 0 0 0 0 0 0 0 0
## HG00246 1 0 0 0 0 0 0 0 0 0
## HG00250 1 0 0 0 0 0 0 0 0 0
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## HG00273 1 0 0 0 0 0 0 0 0 0
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## HG00278 1 0 0 0 0 0 0 0 0 0
## HG00280 0 0 0 0 0 0 0 0 0 0
## HG00281 1 0 0 0 0 0 0 0 0 0
## HG00282 1 0 0 0 0 0 0 0 0 0
## HG00284 1 0 0 0 0 0 0 0 0 0
## HG00285 1 0 0 0 0 0 0 0 0 0
## HG00288 1 0 0 0 0 0 0 0 0 0
## HG00290 1 0 0 0 0 0 0 0 0 0
## HG00304 1 0 0 0 0 0 0 0 0 0
## HG00306 1 0 0 0 0 0 0 0 0 0
## HG00308 1 0 0 0 0 0 0 0 0 0
## HG00309 1 0 0 0 0 0 0 0 0 0
## HG00310 0 0 0 0 0 0 0 0 0 0
## HG00311 1 0 0 0 0 0 0 0 0 0
## HG00313 0 0 0 0 0 0 0 0 0 0
## HG00315 0 0 0 0 0 0 0 0 0 0
## HG00318 0 0 0 0 0 0 0 0 0 0
## HG00319 1 0 0 0 0 0 0 0 0 0
## HG00320 1 0 0 0 0 0 0 0 0 0
## HG00321 0 0 0 0 0 0 0 0 0 0
## HG00323 1 0 0 0 0 0 0 0 0 0
## HG00324 1 0 0 0 0 0 0 0 0 0
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## HG00329 0 0 0 0 0 0 0 0 0 0
## HG00330 1 0 0 0 0 0 0 0 0 0
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## HG00335 1 0 0 0 0 0 0 0 0 0
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## HG00341 1 0 0 0 0 0 0 0 0 0
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## HG00343 0 0 0 0 0 0 0 0 0 0
## HG00344 1 0 0 0 0 0 0 0 0 0
## HG00345 1 0 0 0 0 0 0 0 0 0
## HG00346 1 0 0 0 0 0 0 0 0 0
## HG00349 1 0 0 0 0 0 0 0 0 0
## HG00350 0 0 0 0 0 0 0 0 0 0
## HG00351 1 0 0 0 0 0 0 0 0 0
## HG00353 1 0 0 0 0 0 0 0 0 0
## HG00355 1 0 0 0 0 0 0 0 0 0
## HG00356 1 0 0 0 0 0 0 0 0 0
## HG00357 1 0 0 0 0 0 0 0 0 0
## HG00358 0 0 0 0 0 0 0 0 0 0
## HG00360 1 0 0 0 0 0 0 0 0 0
## HG00361 1 0 0 0 0 0 0 0 0 0
## HG00362 1 0 0 0 0 0 0 0 0 0
## HG00364 1 0 0 0 0 0 0 0 0 0
## HG00365 0 0 0 0 0 0 0 0 0 0
## HG00366 1 0 0 0 0 0 0 0 0 0
## HG00367 1 0 0 0 0 0 0 0 0 0
## HG00368 0 0 0 0 0 0 0 0 0 0
## HG00369 0 0 0 0 0 0 0 0 0 0
## HG00371 1 0 0 0 0 0 0 0 0 0
## HG00372 1 0 0 0 0 0 0 0 0 0
## HG00373 1 0 0 0 0 0 0 0 0 0
## HG00375 1 0 0 0 0 0 0 0 0 0
## [,198] [,199] [,200] [,201] [,202] [,203] [,204] [,205] [,206] [,207]
## HG00096 0 0 0 0 0 0 0 0 0 0
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## HG00101 0 0 0 0 0 0 0 0 0 0
## HG00102 0 0 0 0 0 0 0 0 0 0
## HG00103 0 0 0 0 0 0 0 0 0 0
## HG00105 0 0 0 0 0 0 0 0 0 0
## HG00106 0 0 0 0 0 0 0 0 0 0
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## HG00110 0 0 0 0 0 0 0 0 0 0
## HG00111 0 0 0 0 0 0 0 0 0 0
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## HG00119 0 0 0 0 0 0 0 0 0 0
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## HG00130 0 0 0 0 0 0 0 0 0 0
## HG00131 0 0 0 0 0 0 0 0 0 0
## HG00132 0 0 0 0 0 0 0 0 0 0
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## HG00136 0 0 0 0 0 0 0 0 0 0
## HG00137 0 0 0 0 0 0 0 0 0 0
## HG00138 0 0 0 0 0 0 0 0 0 0
## HG00139 0 0 0 0 0 0 0 0 0 0
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## HG00318 0 0 0 0 0 0 0 0 0 0
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## HG00345 0 0 0 0 0 0 0 0 1 0
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## HG00353 0 0 0 0 0 0 0 0 1 0
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## HG00360 0 0 0 0 0 0 0 0 0 0
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## [,208] [,209] [,210] [,211] [,212] [,213] [,214] [,215] [,216] [,217]
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## HG00159 0 0 0 0 0 0 0 0 0 0
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## [,218] [,219] [,220] [,221] [,222] [,223] [,224] [,225] [,226] [,227]
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## [,228] [,229] [,230] [,231] [,232] [,233] [,234] [,235] [,236] [,237]
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## [,258] [,259] [,260] [,261] [,262] [,263] [,264] [,265] [,266] [,267]
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## HG00281 0 0 0 0 0 0 0 0 0 0
## HG00282 0 0 0 0 0 0 0 0 0 0
## HG00284 0 0 0 0 0 0 0 0 0 0
## HG00285 0 0 0 0 0 0 0 0 0 0
## HG00288 0 0 0 0 0 0 0 0 0 0
## HG00290 0 0 0 0 0 0 0 0 0 0
## HG00304 0 0 0 0 0 0 0 0 0 0
## HG00306 0 0 0 0 0 0 0 0 0 0
## HG00308 0 0 0 0 0 0 0 0 0 0
## HG00309 0 0 0 0 0 0 0 0 0 1
## HG00310 0 0 0 0 0 0 0 0 0 0
## HG00311 0 0 0 0 0 0 0 0 0 0
## HG00313 0 0 0 0 0 0 0 0 0 0
## HG00315 0 0 0 0 0 0 0 0 0 0
## HG00318 0 0 0 0 0 0 0 0 0 0
## HG00319 0 0 0 0 0 0 0 0 0 0
## HG00320 0 0 0 0 0 0 0 0 0 1
## HG00321 0 0 0 0 0 0 0 0 0 0
## HG00323 0 0 0 0 0 0 0 0 0 0
## HG00324 0 0 0 0 0 0 0 0 0 0
## HG00325 0 0 0 0 0 0 0 0 0 0
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## HG00328 0 0 0 0 0 0 0 0 0 1
## HG00329 0 0 0 0 0 0 0 0 0 0
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## HG00343 0 0 0 0 0 0 0 0 0 0
## HG00344 0 0 0 0 0 0 0 0 0 0
## HG00345 0 0 0 0 0 0 0 0 0 0
## HG00346 0 0 0 0 0 0 0 0 0 0
## HG00349 0 0 0 0 0 0 0 0 0 0
## HG00350 0 0 0 0 0 0 0 0 0 0
## HG00351 0 0 1 0 0 0 0 0 0 0
## HG00353 0 0 0 0 0 0 0 0 0 0
## HG00355 0 0 0 0 0 0 0 0 0 0
## HG00356 0 0 0 0 0 0 0 0 0 0
## HG00357 0 0 0 0 0 0 0 0 0 0
## HG00358 0 0 0 0 0 0 0 0 0 0
## HG00360 0 0 0 0 0 0 0 0 0 0
## HG00361 0 0 0 0 0 0 0 0 0 1
## HG00362 0 0 0 0 0 0 0 0 0 0
## HG00364 0 0 0 0 0 0 0 0 0 0
## HG00365 0 0 0 0 0 0 0 0 0 0
## HG00366 0 0 0 0 0 0 0 0 0 0
## HG00367 0 0 0 0 0 0 0 0 0 0
## HG00368 0 0 0 0 0 0 0 0 0 0
## HG00369 0 0 0 0 0 0 0 0 0 0
## HG00371 0 0 0 0 0 0 0 0 0 0
## HG00372 0 0 0 0 0 0 0 0 0 0
## HG00373 0 0 0 0 0 0 0 0 0 0
## HG00375 0 0 0 0 0 0 0 0 0 0
## [,348] [,349] [,350] [,351] [,352] [,353] [,354] [,355] [,356] [,357]
## HG00096 0 0 0 0 0 0 0 0 0 0
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## HG00118 0 0 0 0 0 0 0 0 0 0
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## HG00159 0 0 0 0 0 0 0 0 0 0
## HG00160 0 0 0 0 0 0 0 0 0 0
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## HG00244 0 0 0 0 0 0 0 0 0 0
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## HG00371 1 1 0 0 0 0 0 0 0 0
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## [,358] [,359] [,360] [,361] [,362] [,363] [,364] [,365] [,366] [,367]
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## HG00158 1 0 0 0 0 0 0 0 1 0
## HG00159 0 0 0 0 0 0 0 0 0 0
## HG00160 1 0 0 0 0 0 0 0 1 0
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## HG00178 1 0 0 0 0 0 0 0 1 0
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## HG00180 0 0 0 0 0 0 0 0 0 0
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## HG00246 1 0 0 0 0 0 0 0 1 0
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## [,368] [,369] [,370] [,371] [,372] [,373] [,374] [,375] [,376] [,377]
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## HG00357 0 0 0 0 0 0 0 0 1 0
## HG00358 0 0 0 0 0 0 0 0 0 0
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## HG00361 0 0 0 0 0 0 0 0 1 0
## HG00362 0 0 0 1 0 0 0 1 1 0
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## [,378] [,379] [,380] [,381] [,382] [,383] [,384] [,385] [,386] [,387]
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## [,388] [,389] [,390] [,391] [,392] [,393] [,394] [,395] [,396] [,397]
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## [,398] [,399] [,400] [,401] [,402] [,403] [,404] [,405] [,406] [,407]
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## [ reached getOption("max.print") -- omitted 2327 rows ]dim(no_NA)## [1] 2504 563Including Plots
You can also embed plots, for example:
Note that the echo = FALSE parameter was added to the
code chunk to prevent printing of the R code that generated the
plot.