Question: find genes near a microRNA binding site
gravatar for pengu447
3 months ago by
pengu4470 wrote:

Hello, I have got 2 dataframes in R. One with informations about my genes (columns: gene-id, startposition, endposition, strand, chromosome) and the other one with informations about the microRNAs (columns: id, startposition, endposition, strand, chromosome). I want to find out which genes are near a binding site of the microRNAs but I don't know how to do that in R. (I am new at using R) Is there a package which I can use by chance?

Thank you a lot for answering!!

microrna R genes binding site • 87 views
ADD COMMENTlink written 3 months ago by pengu4470

In Bioconductor we would generally convert these types of data.frames into a GRange object from the GenomicRanges package. There are many built in functions for comparing GRange objects; I suggest looking at the user manual and look at the functions like findOverlaps or the section on nearest-methods for "Finding the nearest genomic range neighbor".

ADD REPLYlink written 3 months ago by shepherl ♦♦ 1.5k
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