Hi all,
When I remove the gene version numbers from from the ENSG ID, those genes with the, "_PAR_", suffix e.g.
"ENSG00000002586.20_PAR_Y" "ENSG00000124333.16_PAR_Y" "ENSG00000124334.17_PAR_Y" "ENSG00000167393.18_PAR_Y" "ENSG00000169084.15_PAR_Y"
aren't being removed. I have tried using the following (obtained from stack) with no success
str_replace(rownames(data), pattern = ".[0-9]+$", replacement = "")
gsub("\\..*","", rownames(data))
tools::file_path_sans_ext(rownames(data))
But these troublesome gene versions remain. Any thoughts?
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BioInfoBeginner •
This pattern: str_replace(rownames(data), pattern = ".[0-9]+$", replacement = "") removes any trailing numbers from a string, and one character before where the number sequence starts. It fails because none of these IDs end in a number.
This pattern: gsub("\\..*","", rownames(data)) removes the first period and everything following it, and in fact it should work fine:
> gsub('\\..*', '', 'ENSG00000213123.16_PAR_Y')
[1] "ENSG00000213123"
could it be that you forgot to reassign the rownames, i.e.:
rownames(data) <- gsub("\\..*","", rownames(data))
?
Thanks for the explanations LChart. Regrettably, reassigning is not missing from my script.
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