CNV plot using cn.mops
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ari • 0
@ari-22541
Last seen 2.7 years ago

Hello: I would like to create some CNV plots for my NGS data. My data (data_frame, actually) looks like this:

chrom position 100245 11092 111790 114305 1 36467771 -0,307932159 -0,207763663 -0,444455669 0,220965487 1 43337797 -0,473760058 -0,253017844 -0,353509972 0,108565563 1 43338044 -0,420558333 -0,235032874 -0,490550169 0,075824818 1 43338510 -0,341944732 -0,351597737 -0,344720128 0,120010005 1 43339239 -0,303916253 -0,256456979 -0,226249326 -0,02799505 1 43339924 -0,37444769 -0,206704965 -0,400419957 0,036812075 1 43340329 -0,368610889 -0,153135645 -0,343051321 0,175352736 1 43346416 -0,219898315 -0,23232204 -0,261116906 0,088929747 1 43346742 -0,366113383 -0,265546314 -0,323953814 -0,016848497 ...

Sorry for the bad formatting, but each column label should be aligned with its corresponding values (chrom-->1, position -->36467771, etc) I am trying to use the cn.mops R package. In the documentation, it is mentioned that the input file can be either BAM or a read count matrix. I am trying to run the script with my data. The labels are as follows: "chrom" is the chromosome number (from 1 to X and Y), "position" is the start position, and the "100245, 11092" are sample numbers, each one with the numeric values (normalised and log ratio) of the read counts obtained. I am trying to use cn.mops to create a CNV plot for every sample against all the chromosomes. The goal is to get several plots (one for each sample), with the CNV representation, like the first graphic shown here: https://cnvkit.readthedocs.io/en/stable/plots.html But the first error I am getting when using cn.mops is: "All values must be greater or equal zero and finite." ¿Is my data format wrongly formatted to use cn.mops R package? I have tried to use several other R libraries, but I'm afraid the problem lies within my starting data.

I would very appreciate some additional help (or info about R packages that can generate plots like the ones I am looking for). Thanks in advance!

cnv R plot visualization cn.mops software error • 403 views
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EDIT: The data frame was not correctly formatted, this is the actual data:

chrom   position    100245  11092   111790  114305
1   36467771    -0,307932159    -0,207763663    -0,444455669    0,220965487
1   43337797    -0,473760058    -0,253017844    -0,353509972    0,108565563


... up to chromosome X and Y