cellularity #11
Description
Dear developers, I ran into 2 questions for v1.0.8. Any suggestion will be highly appreciated. Many thanks!
Q1. An error message:
Error in prop.test(v$mut.count[i], v$mut.count[i] + v$WT.count[i], e[i], : not enough data
The reason might be line 595 does not return a value for cellularity:
prop.test needs expected.burden.for.MCN.
expected.burden.for.MCN needs cellularity.
In the processing.R file, line 667: cellularity = GetCellularity(cellularity_file).
The return line for GetCellularity on line 595: return(d['FRAC_GENOME','rho'])
This line does not seem to return a single value for cellularity.
The processing.R file is found here (https://github.com/Wedge-lab/dpclust3p/blob/master/R/preprocessing.R)
Q2 (might not be an issue if processing.R work properly)
Ran processing.R by manually set cellularity value on the T2-128X demo data (https://www.nature.com/articles/s41592-020-01013-2). Got 52 mutations as "NA". Is it expected to be "NA", if the mutation position is not covered by the CNV file; or is it expected to be calculated by assuming copy number is total 2, major 2, minor 0?