qualityScoreBySnp: Mean and median quality score for SNPs

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

View source: R/qualityScoreBySnp.R

Description

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

Usage

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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

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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)

GWASTools documentation built on Nov. 8, 2020, 7:49 p.m.