How to highlight a subset of SNPs on a Manhattan plot

Questions about GenABEL (aka *ABEL) suite of packages
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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")
##assoc using kinship matrix
##subset out 1 SNP

Thanks for any help!

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