qualityScoreBySnp: Mean and median quality score for SNPs
In 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 scans with a non-missing genotype call, for each SNP.

1 2	qualityScoreBySnp(intenData, genoData, scan.exclude = NULL, block.size = 5000, verbose = TRUE)

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