seqminer (version 7.1)

[.PlinkFile: Read a gene from BGEN file and return a genotype matrix

Description

Read a gene from BGEN file and return a genotype matrix

Usage

# S3 method for PlinkFile
[(plinkFileObject, sampleIndex, markerIndex)

Arguments

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

Value

genotype matrix, marker by sample

See Also

http://zhanxw.com/seqminer/ for online manual and examples

Examples

# NOT RUN {
## 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]
# }