Failed to set argument `-f/--fracs` in `dxm_solveMethylation`

[nshen7]

Hello @jfong1123 ,

I'm analyzing a bisulfite sequencing data with DXM, but I encountered an error while using the -f/--fracs argument in the function dxm_solveMethylation. Here is the test code with the example data incorporated in DXM package:

/home/nshen7/.local/bin/dxm_solveMethylation \ -f 1 \ -i /arc/project/st-kdkortha-1/nshen7/software/dxm/example_data/sampleInput.bed \ -o data/test/testSample

And following is the error output :

usage: dxm_solveMethylation [-h] -i INFILE [-o OUTPREF] [-c MAXCOVERAGE] [-m MAXSUBPOP] [-f {0,1,2}] [-u USERSUPPLIEDFRACFILE] [-b BINFILE] [-q FREQFILE] dxm_solveMethylation: error: argument -f/--fracs: invalid choice: '1' (choose from 0, 1, 2)

Could you take a look into it?

Many thanks in advance!

Ning

[jredwards417]

Apologies for not seeing this sooner! This should be all fixed in the version I just uploaded. Please let me know if you run into other issues.

A few notes in case it is useful:

• In general we have found using the default (-f 0) choices for the fractions works very well.
• Using -f 1 will not work well for the test case in the example data, since it was designed to be a light weight test to be sure the installation worked. The code will run, but the answer may be unsatisfying.
• If you want to estimate the fractions directly from your data, we recommend estimating the cell fractions from a subset of regions that differ between the underlying cell types identified from an external data source rather than try to estimate them across the entire dataset.