GenABEL (version 1.8-0)

redundant: 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

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

See Also

check.marker

Examples

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