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I have a data frame (named as df) with single column of protein IDs and other file with two columns of protein IDs (named as df1). I need to find the df IDs present in either first or second column of df1 and extract corresponding Id from the df1.

df = data.frame(p = c("ENSG00000198400","ENSG00000066044","ENSG00000188612","ENSG00000177606","ENSG00000146648"))
df1 = data.frame(p1 = c("ENSG00000105647","ENSG00000110395","ENSG00000165119","ENSG00000160293","ENSG00000198400","ENSG00000198400"),p2 = c("ENSG00000198400","ENSG00000198400","ENSG00000198400","ENSG00000142949","ENSG00000112936","ENSG00000162434"))

Sample output:

df2= data.frame(p = c("ENSG00000198400","ENSG00000198400","ENSG00000198400","ENSG00000198400","ENSG00000198400"),p2 = c("ENSG00000105647","ENSG00000110395","ENSG00000165119","ENSG00000112936","ENSG00000162434"))
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  • $\begingroup$ This seems to be an XY problem. Can you give us an idea of your bigger picture problem? $\endgroup$
    – Ram RS
    Oct 17, 2022 at 20:29
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    $\begingroup$ I'd say this belongs on Stack Overflow as is more of a pure coding problem - and you'll get a faster response there. I'd suggest deleting this and reposting here. $\endgroup$
    – user438383
    Oct 17, 2022 at 20:51
  • $\begingroup$ Gene names... looks like there's a biology aspect to this; adding more context to the question would make it more obviously bioinformatics. $\endgroup$
    – gringer ♦
    Oct 18, 2022 at 20:33

1 Answer 1

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you can try this:

df = data.frame(p = c("ENSG00000198400","ENSG00000066044","ENSG00000188612",
                       "ENSG00000177606","ENSG00000146648"))
df1 = data.frame(p1 = c("ENSG00000105647","ENSG00000110395","ENSG00000165119",
                         "ENSG00000160293","ENSG00000198400","ENSG00000198400"),
                 p2 = c("ENSG00000198400","ENSG00000198400","ENSG00000198400",
                         "ENSG00000142949","ENSG00000112936","ENSG00000162434"))

df2 = rbind(df1[df1$p1 %in% df$p,],df1[df1$p2 %in% df$p,])

df2 <- transform(df2, p2 = ifelse(df2$p2%in%df$p, p1, p2), p1 = ifelse(df2$p2%in%df$p, p2, p1))
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