R: function to do redundancy check

redundant {GenABEL} | R Documentation

## function to do redundancy check

### Description

Checks marker redundancy, understood as comcordance between genotypic distributions (including missing values)

### Usage

    redundant(data, pairs = "bychrom", minconcordance = 2.0)

### Arguments

`data` | gwaa.data or snp.data object
`pairs` | "bychrom" or "all" to check pairs within chromosome only or genome-wide
`minconcordance` | find "redundant" pairs of markers with concordance >= "minconcordance". If "minconcordance" is more then 1.0, only pairs of markers which are exactly the same (independent of coding), including NA pattern, are considered as redundant. If "minconcordance" is <= 1, the concordance rate is computed as percent of genotypes which are the same, including the genotypes with NA. I.e. if both genotypes are NA, this is counted as a match, if one is NA and other is measured, this is counted as dismatch. Note that option with "minconcordance" <= 1 takes much longer time to run.

### Value

A list containing reference SNP as a name and all SNPs which has "the same" genotypic distribution as values:

`"refSNP1"` | SNP11, SNP12, ...
`"refSNP2"` | SNP21, SNP22, ...
`...` | etc.
`"refSNPlast"` | SNPlast1, SNPlast2, ...
`"all"` | list of all redundant SNPs, which can be dropped from consideration

### Author(s)

Yurii Aulchenko

### See Also

`check.marker`

### Examples

    require(GenABEL.data)
    data(srdta)
    redundant(srdta@gtdata)
    redundant(srdta@gtdata[,1:50],minconcordance=0.8)

[Package GenABEL version 1.8-0 Index]