function to subset objects of class scan.gwaa and check.marker

snp.subset {GenABEL}R Documentation

function to subset objects of class scan.gwaa and check.marker

Description

Computing objects of class scan.gwaa may take long, especially when haplotypic analysis is performed. Therefore this function helps substracting results on some region (indicated by list of SNPs)

Usage

snp.subset(data, snpsubset)

Arguments

data object of class scan.gwaa-class or check.marker-class
snpsubset character vector of snps to select

Value

Object of class scan.gwaa-class or check.marker-class

Author(s)

Yurii Aulchenko

See Also

scan.gwaa-class, check.marker-class

Examples

data(srdta)
# processing check.marker object
#mc <- check.marker(data=srdta@gtdata[,1:100],redundant="all",maf=0.01,minconcordance=0.9,fdr=.1,ibs.mrk=0)
mc <- check.marker(data=srdta@gtdata[,1:100],maf=0.01,fdr=.1,ibs.mrk=0)
summary(mc)
#plot(mc)
mc1 <- snp.subset(mc,snps=srdta@gtdata@snpnames[20:50])
summary(mc1)
#plot(mc1)
# processing scan.gwaa object
a <- qtscore(qt3~sex+age,data=srdta)
plot(a)
a1 <- snp.subset(a,snps=srdta@gtdata@snpnames[10:20])
plot(a1)

[Package GenABEL version 1.6-7 Index]