qualityScoreBySnp: Mean and median quality score for SNPs

In smgogarten/GWASTools: Tools for Genome Wide Association Studies

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.

Details

intenData and genoData must have matching snpID and scanID.

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.

Author(s)

Cathy Laurie

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)

smgogarten/GWASTools documentation built on July 4, 2023, 2:32 a.m.