duplicateDiscordance {GWASTools} | R Documentation

## Duplicate discordance

### Description

A function to compute pair-wise genotype discordances between multiple genotyping instances of the same subject.

### Usage

    duplicateDiscordance(genoData, subjName.col,
                         one.pair.per.subj=TRUE, corr.by.snp=FALSE,
                         minor.allele.only=FALSE, allele.freq=NULL,
                         scan.exclude=NULL, snp.exclude=NULL,
                         snp.block.size=5000, verbose=TRUE)

### Arguments

`genoData` | `GenotypeData` object
`subjName.col` | A character string indicating the name of the annotation variable that will be identical for duplicate scans.
`one.pair.per.subj` | A logical indicating whether a single pair of scans should be randomly selected for each subject with more than 2 scans.
`corr.by.snp` | A logical indicating whether correlation by SNP should be computed (may significantly increase run time).
`minor.allele.only` | A logical indicating whether discordance should be calculated only between pairs of scans in which at least one scan has a genotype with the minor allele (i.e., exclude major allele homozygotes).
`allele.freq` | A numeric vector with the frequency of the A allele for each SNP in `genoData`. Required if `minor.allele.only=TRUE`.
`scan.exclude` | An integer vector containing the ids of scans to be excluded.
`snp.exclude` | An integer vector containing the ids of SNPs to be excluded.
`snp.block.size` | Integer block size for SNPs if `corr.by.snp=TRUE`.
`verbose` | Logical value specifying whether to show progress information.

### Details

`duplicateDiscordance` calculates discordance metrics both by scan and by SNP. If `one.pair.per.subj=TRUE` (the default), each subject with more than two duplicate genotyping instances will have two scans randomly selected for computing discordance. If `one.pair.per.subj=FALSE`, discordances will be calculated pair-wise for all possible pairs for each subject.

### Value

A list with the following components:

`discordance.by.snp` | data frame with 5 columns: 1. snpID, 2. discordant (number of discordant pairs), 3. npair (number of pairs examined), 4. n.disc.subj (number of subjects with at least one discordance), 5. discord.rate (discordance rate i.e. discordant/npair)
`discordance.by.subject` | a list of matrices (one for each subject) with the pair-wise discordance between the different genotyping instances of the subject
`correlation.by.subject` | a list of matrices (one for each subject) with the pair-wise correlation between the different genotyping instances of thesubject

If `corr.by.snp=TRUE`, `discordance.by.snp` will also have a column "correlation" with the correlation between duplicate subjects. For this calculation, the first two samples per subject are selected.

### Author(s)

Tushar Bhangale, Cathy Laurie, Stephanie Gogarten, Sarah Nelson

### See Also

`GenotypeData`, `duplicateDiscordanceAcrossDatasets`, `duplicateDiscordanceProbability`, `alleleFrequency`

### Examples

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

    disc <- duplicateDiscordance(genoData, subjName.col="subjectID")

    # minor allele discordance
    afreq <- alleleFrequency(genoData)
    minor.disc <- duplicateDiscordance(genoData, subjName.col="subjectID",
      minor.allele.only=TRUE, allele.freq=afreq[,"all"])

    close(genoData)

[Package GWASTools version 1.33.3 Index]