GenABEL (version 1.8-0)

snp.subset: 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

See Also

scan.gwaa-class, check.marker-class

Examples

require(GenABEL.data)
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)