[.PlinkFile {seqminer} | R Documentation |
Read a gene from BGEN file and return a genotype matrix
## S3 method for class 'PlinkFile' plinkFileObject[sampleIndex, markerIndex]
plinkFileObject |
a PlinkFileObject obtained by openPlink() |
sampleIndex |
integer, 1-basd, index of samples to be extracted |
markerIndex |
integer, 1-basd, index of markers to be extracted |
genotype matrix, marker by sample
http://zhanxw.com/seqminer/ for online manual and examples
## these indice are nonsynonymous markers for 1:196621007-196716634", ## refer to the readVCFToMatrixByRange() fileName = system.file("plink/all.anno.filtered.extract.bed", package = "seqminer") filePrefix = sub(fileName, pattern = ".bed", replacement = "") plinkObj = openPlink(filePrefix) sampleIndex = seq(3) markerIndex =c(14, 36) cfh <- plinkObj[sampleIndex, markerIndex]