sub-.PlinkFile: Read from binary PLINK file and return a genotype matrix

In seqminer: Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R

Read from binary PLINK file and return a genotype matrix

Description

Read from binary PLINK file and return a genotype matrix

Usage

## S3 method for class '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

## 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]

seqminer documentation built on Oct. 7, 2024, 1:15 a.m.