Data grouping with DataTrack or AlignmentTrack classes
0
0
Entering edit mode
jma1991 ▴ 60
@jma1991-11856
Last seen 7 days ago
Cumbernauld

I am using Gviz to view ChIP-seq coverage from either BAM files or bigWig files. I would like to group the data by a factor variable (as described on page 21 of the Gviz user guide). However, grouping only seems to work if I pass in a matrix of data values. It doesn't work when I pass in a list of DataTracks created from bigWig files, or AlignmentTracks created from BAM files.

Is there a quick way to create the necessary data matrix from the DataTrack or AlignmentTracks? Similar Gviz: plotting mean values of biological replicates suggest creating a GRanges object of the viewable region and using SummarizeOverlaps to create a count matrix which I would then have to normalise.

gviz gviz-package • 672 views
ADD COMMENT

Login before adding your answer.

Traffic: 324 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