Manipulating Wig File In R,
3
1
Entering edit mode
8.8 years ago

I am new to this file type and rtracklayer package. Now I have a wig file and a matrix with certain ranges(several times the span in wig file) on several specific sites. I want to get average score in my certain ranges on specific sites. Is there any good command in this package I can use ? or any good ways to get a matrix with columns only on start, end, score ? Thanks you in advance guys :)

r wiggle • 4.1k views
ADD COMMENT
1
Entering edit mode
8.8 years ago

I would highly recommend using GenomicRanges: http://www.bioconductor.org/packages/2.11/bioc/html/GenomicRanges.html

It is very easy to construct GRanges objects from WIG files - or any other matrix for that matter, and it has the functions built in that you are looking for (mean/median/sum etc over defined windows).

ADD COMMENT
0
Entering edit mode
8.8 years ago

You could invoke a system command with the *wig tools developed by the UCSC: ( http://hgdownload.cse.ucsc.edu/admin/exe/ ) and grab the results.

ADD COMMENT

Login before adding your answer.

Traffic: 1447 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

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

Powered by the version 2.3.6