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Giovanni Carosso
▴
30
@giovanni-carosso-6254
Last seen 10.3 years ago
Hello,
I have three CSV files of genomic intervals (chromosome start, stop,
plus
other information in different columns) each containing between 10k-
20k
lines.
I am looking for a way to pull out from one file only the lines that
have
genomic overlap with both of the other two files. In other words,
subset
file A to include only the lines of file A whose interval overlaps
intervals in Files B and C.
I'm able to create GRanges and manipulate these to get the subsetted
GRanges list, but I have not found a way to then use this GRanges as
an
index to pull out the proper lines from CSV file.
Is there a simple way to subset my file in this way that I'm missing?
Thanks,
Giovanni
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