Description Usage Arguments Details Value
Reading .raw file that was previously exported from PLINK - see details. Additional information about SNP mapping is read from .map file.
1 2 3 4 5 6 7 8 | screen_snps(
rawFile,
mapFile = "",
phenotype,
pValMax = 0.05,
chunkSize = 100,
verbose = TRUE
)
|
rawFile |
character, name of .raw file |
mapFile |
character, name of .map file |
phenotype |
numeric vector or an object of class |
pValMax |
numeric, p-value threshold value used for screening |
chunkSize |
integer, number of snps that will be processed together. The bigger chunkSize is, the faster function works but computer might run out of RAM |
verbose |
if TRUE (default) information about progress is printed |
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:
http://pngu.mgh.harvard.edu/~purcell/plink/dataman.shtml
object of class screeningResult
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