qualityScoreBySnp {GWASTools} | R Documentation |
This function calculates the mean and median quality score, over all scans with a non-missing genotype call, for each SNP.
qualityScoreBySnp(intenData, genoData, scan.exclude = NULL, block.size = 5000, verbose = TRUE)
intenData |
|
genoData |
|
scan.exclude |
An integer vector containing the id's of scans to be excluded. |
block.size |
Number of SNPs to be read from intenData and genoData at once. |
verbose |
Logical value specifying whether to show progress information. |
intenData
and genoData
must have matching snpID
and scanID.
The function returns a matrix with the following columns:
mean.quality |
A vector of mean quality scores for each snp. |
median.quality |
A vector of median quality scores for each snp. |
Cathy Laurie
IntensityData
, GenotypeData
, qualityScoreByScan
qualfile <- system.file("extdata", "illumina_qxy.gds", package="GWASdata") qual <- GdsIntensityReader(qualfile) qualData <- IntensityData(qual) genofile <- system.file("extdata", "illumina_geno.gds", package="GWASdata") geno <- GdsGenotypeReader(genofile) genoData <- GenotypeData(geno) quality <- qualityScoreBySnp(qualData, genoData) close(qualData) close(genoData)