R: Read from binary PLINK file and return a genotype matrix

[.PlinkFile {seqminer} | R Documentation

## 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]

[Package seqminer version 8.0 Index]