screen_snps: Reading and screening SNPs from .raw file and

In geneSLOPE: Genome-Wide Association Study with SLOPE

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
)

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

Value

object of class screeningResult.

geneSLOPE documentation built on Aug. 16, 2023, 5:10 p.m.