Error plotting matrix

[rpetroll]

Hi,

I am trying to plot a matrix heatmap including all chromosomes. I was able to import my .mcool file as an HiCExperiment object. But when trying to execute the plotMatrix argument, I am receiving the following error:

hic <- import(cf, format = "mcool")
hic

HiCExperiment object with 24,599,023 contacts over 1,195,338 regions
fileName: "spec1.final.mcool"
focus: "whole genome"
resolutions(10): 1000 5000 ... 1000000 2500000
active resolution: 1000
interactions: 13468294
scores(2): count balanced
topologicalFeatures: compartments(0) borders(0) loops(0) viewpoints(0)
pairsFile: N/A
metadata(0):

plotMatrix(hic, use.scores = 'balanced')

Error in if (fraction_ov > 0.9) { : missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In all.as + all.ae : NAs produced by integer overflow
2: In all.as + all.ae : NAs produced by integer overflow
3: In GenomicRanges::width(bbOne) + GenomicRanges::width(bbTwo) :
NAs produced by integer overflow

Thanks a lot for your help!
Best,
Romy

[js2264]

Hi Romy,
This issue could arise from the fact that you matrix (seems) quite sparse, seeing you have ~1.2M regions and 13M interactions (pixels). Can you try plotting with plotMatrix(hic, use.scores = 'balanced', symmetrical = FALSE) ? This would skip the fraction_ov computation but should return only a triangular matrix.

Also, you are working with a pretty large genome (1.2M *1kb = 1.2Gb), and if you want to plot the genome-wide matrix, I would suggest importing the file with a lower resolution (eg 1000000) to try and plot it. I would guess the 1000 resolution is probably why you have this issue arising.