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I need to find the genes that overlap deletions and point mutations that I found in my analysis. I have a file with a list of repair genes, I have 3 files:

  • A list of repair genes RepairGenes.bed
  • A list of deletions Deletions.tsv
  • A list of point mutations PointMutation.pm

RepairGnes.bed

start   end         Name
133589333   133763062   ABL1
105235686   105262088   AKT1
40736224    40791443    AKT2
109525996   109531436   ALKBH2

Deletions.tsv

start   end
1823208 1831709
3631182 3661599
127006  135852
2089816 2097867

PointMuation.pm

position
396264 
774520 
774692 
1574863

I need to find the list of all genes that overlap (think like an intersection between two sets) RepairGenes.bed, Deletions.tsv and PointMutation.pm.
I've tried a bunch of package from Biocondictor like IRanges and GenesOverlap but they seems to do something else.
Does anyone know how can I deal with this task?

Federico Grandi
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Giuseppe Minardi
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  • Can you add example of wanted output and files using `dput` function. – pogibas Jan 06 '19 at 22:08
  • The output should be the rows of RepairGenes.bed that have an overlap in Deletion.tsv – Giuseppe Minardi Jan 06 '19 at 22:12
  • So what's about PointMutation? Please read and edit your question according to: [How to make a great R reproducible example?](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example). Also, there's no chromosome information. – pogibas Jan 06 '19 at 22:13
  • Thank you, Maybe I'm not that clear in the question, I'm going got edit it. The point mutations file is needed because, after filtering RepairGenes.bed looking at the overlapping deletion I have to filter again RepairGenes.bed keeping only rows where the position in point mutation intersect RepairGenes.bed. – Giuseppe Minardi Jan 06 '19 at 22:17
  • `GenomicRanges::findOverlaps` or `data.table::foverlaps` should work for this. What have you tried and failed, please share the code. – zx8754 Jan 07 '19 at 10:04

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