qualityScoreBySnp {GWASTools} | R Documentation

## 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)

[Package GWASTools version 1.30.1 Index]