How to mark points on a Manhattan plot?
I am using the qqman package and have some labeling questions in the qqman package. I ran the following command in R:
manhattan(mydata, chr = "CHR", bp = "MAPINFO", p = "P.Value", snp = "SNP", col = c("blue4", "orange3"), chrlabs = NULL,suggestiveline = -log10(1e-05), genomewideline = -log10(5e-08), highlight =NULL, logp = TRUE )
And got a Manhattan plot, but I want to mark all the points with –log10(p) > 20
(which is on the y-axis) according to the "Gene" column in the "mydata" file. This column (Gene) includes gene names, not SNP coordinates (rs ...). Does this column have to be numeric or symbol?
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