Question: metagene: strand orientation of plot?
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gravatar for anton.kratz
2.4 years ago by
anton.kratz50
United States, San Diego, UCSD
anton.kratz50 wrote:

I am using the metagene package (http://www.bioconductor.org/packages/release/bioc/html/metagene.html) by Charles Joly Beauparlant and others. I would like to know if the plot considers strand orientation or not. I.e. the genomic regions used as input might be on the plus or on the minus strand. Now when the package generates the final plot, are the genomic ranges oriented in the same direction in the plot, or not?

Reaching out in the hope to get an answer from someone who uses this package, or maybe the devloper might even read this. Thank you.

 

--

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"

Ubuntu 16.04.1 LTS

metagene • 419 views
ADD COMMENTlink modified 2.4 years ago by Charles Joly Beauparlant160 • written 2.4 years ago by anton.kratz50
Answer: metagene: strand orientation of plot?
3
gravatar for Charles Joly Beauparlant
2.4 years ago by
Canada
Charles Joly Beauparlant160 wrote:

Hello Anton,

By default, the strand orientation is not taken into account. But you do have the option to flip the regions based on the strand during the production of the matrices:

mg <- metagene$new(regions = regions, bam_files = bam_files)

mg$produce_matrices(flip_regions = TRUE)

Cheers!

Charles.

ADD COMMENTlink written 2.4 years ago by Charles Joly Beauparlant160
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