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 -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2020-05-19 at 11.11.43 AM.png Type: image/png Size: 82674 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20200519/0d923656/attachment.png>
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 at 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
Hi Michael, can you please send me code how that would be done? Thanks Ana On Tue, May 19, 2020 at 11:18 AM Michael Dewey <lists at dewey.myzen.co.uk> wrote:> > 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 at 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