How to highlight a subset of SNPs on a Manhattan plot

Questions about GenABEL (aka *ABEL) suite of packages
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finn0100
Posts: 1
Joined: Thu May 08, 2014 9:50 pm

How to highlight a subset of SNPs on a Manhattan plot

Postby finn0100 » Thu May 08, 2014 9:59 pm

Is there a way to highlight a subset of SNPs using the points function on a GenABLE subsetting scan.gwaa dataframe? I have tried the following code and, although I don't receive an error, the SNP I want to highlight does not appear green:
I have 99 individuals and I'm interested in highlighting 1 SNP on the GWAS:

##Kinship matrix
data1.gkin<-ibs(data1[,df@gtdata@chromosome !="X"],weight="freq")
tmp.gkin<-data1.gkin
diag(tmp.gkin)<-hom(data1[,autosomal(data1)])$Var
##assoc using kinship matrix
KIN<-egscore(disease~sex,data=data1,kin=tmp.gkin)
##subset out 1 SNP
ssubs<-data1[1:99,c("30_29683163")]
snp30qt<-qtscore(disease~sex,data=ssubs)
##plot
plot(KIN,col=c("purple","blue"),main="",pch=19,cex=.8,df="1",ylim=c(0,7))
points(snp30qt[,"P1df"],col="forestgreen")


Thanks for any help!

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