snp.subset {GenABEL} | R Documentation |
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)
snp.subset(data, snpsubset)
data |
object of class scan.gwaa-class or check.marker-class |
snpsubset |
character vector of snps to select |
Object of class scan.gwaa-class
or check.marker-class
Yurii Aulchenko
scan.gwaa-class
,
check.marker-class
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)