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

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.