qualityScoreByScan: Mean and median quality score for scans
In amstilp/GWASTools: Tools for Genome Wide Association Studies

Description Usage Arguments Details Value Author(s) See Also Examples

This function calculates the mean and median quality score, over all SNPs with a non-missing genotype call, for each scan.

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qualityScoreByScan(intenData, genoData,
                   snp.exclude = NULL,
                   verbose = TRUE)

`intenData`	`IntensityData` object
`genoData`	`GenotypeData` object
`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)