redundant {GenABEL} | R Documentation |
Checks marker redundancy, understood as comcordance between genotypic distributions (including missing values)
redundant(data, pairs = "bychrom", minconcordance = 2.0)
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. |
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 |
Yurii Aulchenko
data(srdta) redundant(srdta@gtdata) redundant(srdta@gtdata[,1:50],minconcordance=0.8)