qualityScoreByScan {GWASTools} | R Documentation

## Mean and median quality score for scans

### Description

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

### Usage

    qualityScoreByScan(intenData, genoData,
                       snp.exclude = NULL,
                       verbose = TRUE)

### Arguments

`intenData` | `IntensityData` object
`genoData` | `GenotypeData` object
`snp.exclude` | An integer vector containing the id's of SNPs to be excluded.
`verbose` | Logical value specifying whether to show progress information.

### Details

`intenData` and `genoData` must have matching snpID and scanID. Y chromosome SNPs are excluded for females. A "sex" variable must be present in the scan annotation slot of `intenData` or `genoData`.

### Value

The function returns a matrix with the following columns:

`mean.quality` | A vector of mean quality scores for each scan
`median.quality` | A vector of median quality scores for each scan.

### Author(s)

Cathy Laurie

### See Also

`IntensityData`, `GenotypeData`, `qualityScoreBySnp`

### Examples

    library(GWASdata)
    qualfile <- system.file("extdata", "illumina_qxy.gds", package="GWASdata")
    qual <- GdsIntensityReader(qualfile)
    # need scan annotation with sex
    data(illuminaScanADF)
    qualData <- IntensityData(qual, scanAnnot=illuminaScanADF)

    genofile <- system.file("extdata", "illumina_geno.gds", package="GWASdata")
    geno <- GdsGenotypeReader(genofile)
    genoData <- GenotypeData(geno, scanAnnot=illuminaScanADF)

    quality <- qualityScoreByScan(qualData, genoData)
    close(qualData)
    close(genoData)

[Package GWASTools version 1.38.0 Index]