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

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

[Package GenABEL version 1.6-7 Index]