geneSLOPE (version 0.38.2)

screen_snps: Reading and screening SNPs from .raw file and

Description

Reading .raw file that was previously exported from PLINK - see details. Additional information about SNP mapping is read from .map file.

Usage

screen_snps(
  rawFile,
  mapFile = "",
  phenotype,
  pValMax = 0.05,
  chunkSize = 100,
  verbose = TRUE
)

Value

object of class screeningResult.

Arguments

rawFile

character, name of .raw file.

mapFile

character, name of .map file.

phenotype

numeric vector or an object of class phenotypeData.

pValMax

numeric, p-value threshold value used for screening.

chunkSize

integer, number of snps that will be processed together. The bigger the chunkSize is, the faster function works but computer might run out of RAM.

verbose

if TRUE (default) information about progress is printed.

Details

Exporting data from PLINK To import data to R, it needs to be exported from PLINK using the option "--recodeAD" The PLINK command should therefore look like plink --file input --recodeAD --out output. For more information, please refer to: https://zzz.bwh.harvard.edu/plink/dataman.shtml