How to run a function in a r loop

Question

I have a dataframe with a set of genomic co-ordinates. I wish to find genes around those co-ordinates using nearest.gene() which print result one at a time. I have been struggling to run the function in a loop:

apply(gene_lst, 1, function (x) nearest.gene(chr=gene_lst$Chr, pos=gene_lst$Pos))
      1       2       3       4       5       6       7       8       9      10 
"ACBD3" "ACBD3" "ACBD3" "ACBD3" "ACBD3" "ACBD3" "ACBD3" "ACBD3" "ACBD3" "ACBD3"

It is overwriting the first output for the next nine co-ordinates. Is there a better way to run this function?

In your apply function, you didn't pass x into your function nearest.gene() — ThomasIsCoding
– ThomasIsCoding, Commented Feb 5, 2020 at 13:52
That's great! If you think my answer is helpful, please feel free to upvote/accept it. Thanks :) — ThomasIsCoding
– ThomasIsCoding, Commented Feb 8, 2020 at 21:10

ThomasIsCoding · Accepted Answer · 2020-02-05 13:56:06Z

1

I guess you can have a try with the following code, where you should pass x into your function nearest.gene()

apply(gene_lst, 1, function (x) nearest.gene(chr=x["Chr"], pos=x["Pos"]))

answered Feb 5, 2020 at 13:56

ThomasIsCoding

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