find genes near a microRNA binding site

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pengu447 • 0

@pengu447-21299

Last seen 5.4 years ago

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!!

R microRNA genes binding Site • 766 views

ADD COMMENT • link 5.4 years ago pengu447 • 0

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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 REPLY • link 5.4 years ago shepherl 4.1k

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