[R] text annotation on Manhattn plot in qqman

[Michael Dewey]

Dear Ana

Perhaps paste together SNP and GENE using paste() and then supply that 
as the snp parameter.

Michael

On 19/05/2020 17:12, Ana Marija wrote:
> Hello,
> 
> I am making manhattan plot with:
> library(qqman)
> manhattan(a, chr="CHR", bp="BP", snp="SNP", p="P",annotatePval = 0.0001)
> 
> and I would like to annotate these two SNPs which are above the
> threshold so that they have GENE name beside them:
> 
>> a[a$SNP=="rs4081570",]
>          SNP            P CHR       BP GENE
> 1 rs4081570 6.564447e-05  19 15918647 UCA1
>> a[a$SNP=="rs11867934",]
>              SNP            P CHR       BP GENE
> 1021 rs11867934 6.738066e-06  17 16933404 FLCN
> 
> Right now my plot only has SNP name for those 2, how to add GENE names
> (FLCN and UCA1 as well)
> 
> Please advise
> Ana
> 
> 
> 
> ______________________________________________
> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 

-- 
Michael
http://www.dewey.myzen.co.uk/home.html