qualityScoreByScan {GWASTools} | R Documentation |
This function calculates the mean and median quality score, over all SNPs with a non-missing genotype call, for each scan.
qualityScoreByScan(intenData, genoData, snp.exclude = NULL, verbose = TRUE)
intenData |
|
genoData |
|
snp.exclude |
An integer vector containing the id's of SNPs to be excluded. |
verbose |
Logical value specifying whether to show progress information. |
intenData
and genoData
must have matching snpID
and scanID.
Y chromosome SNPs are excluded for females.
A "sex" variable must be present in the scan
annotation slot of intenData
or genoData
.
The function returns a matrix with the following columns:
mean.quality |
A vector of mean quality scores for each scan |
median.quality |
A vector of median quality scores for each scan. |
Cathy Laurie
IntensityData
, GenotypeData
, qualityScoreBySnp
library(GWASdata) qualfile <- system.file("extdata", "illumina_qxy.gds", package="GWASdata") qual <- GdsIntensityReader(qualfile) # need scan annotation with sex data(illuminaScanADF) qualData <- IntensityData(qual, scanAnnot=illuminaScanADF) genofile <- system.file("extdata", "illumina_geno.gds", package="GWASdata") geno <- GdsGenotypeReader(genofile) genoData <- GenotypeData(geno, scanAnnot=illuminaScanADF) quality <- qualityScoreByScan(qualData, genoData) close(qualData) close(genoData)