find genes near a microRNA binding site
Entering edit mode
pengu447 • 0
Last seen 3.2 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 • 297 views
Entering edit mode

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".


Login before adding your answer.

Traffic: 432 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6