GWASTools (version 1.18.0)

qualityScoreBySnp: Mean and median quality score for SNPs

Description

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

Usage

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

Arguments

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.

Value

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.

Details

intenData and genoData must have matching snpID and scanID.

See Also

IntensityData, GenotypeData, qualityScoreByScan

Examples

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)