Which R package is the best to compare and visualise two bed files?

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6.5 years ago

mohamad.merhi96 • 0

I have two bed files 4 columns each , they contain data about transcription factors . I want to compare them in ideograms, to see the common tracks,links , to see where they intersect etc..

Basically I need to do all of the visual analysis on these two, but I'm so confused , which R visual package should I use? There are a lot of them and genuinely I don't know which one is the best

Thanks in advance

R genome visualization visuals • 1.5k views

ADD COMMENT • link 6.5 years ago by mohamad.merhi96 • 0

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I'd suggest starting with a genome browser such as IGV, first. In general, though, unless your genome is very small, you'll end up needing to do something analytical before graphics are meaningful. For that purpose, in R, take a look at GenomicRanges.

ADD REPLY • link 6.5 years ago by Sean Davis 26k

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Yes I was going to suggest GenomicRanges too.

If you want a visual on where your BED regions overlap, load them into the UCSC Genome Browser as Custom Tracks, or use IGV as Seán says.

ADD REPLY • link 6.5 years ago by Kevin Blighe 87k

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