redundant: function to do redundancy check

In GenABEL: genome-wide SNP association analysis

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)

Example output

Loading required package: MASS
Loading required package: GenABEL.data
$all
character(0)

$rs435
[1] "rs455"

$rs663
[1] "rs675"

$rs404
[1] "rs620"

$rs10
[1] "rs29"

$rs611
[1] "rs615"

$rs377
[1] "rs386"

$all
 [1] "rs29"  "rs128" "rs298" "rs332" "rs361" "rs386" "rs388" "rs455" "rs573"
[10] "rs614" "rs615" "rs620" "rs675"

$rs568
[1] "rs573"

$rs73
[1] "rs128" "rs298" "rs332" "rs614"

$rs348
[1] "rs361"

$rs383
[1] "rs388"

GenABEL documentation built on May 30, 2017, 3:36 a.m.