test_bimodal using bed file - empty results

[emblake85]

I am unable to generate test_bimodal results when using --bed_file; it does, however, work with --region. Here is the content of my test.bed.gz file:

chr1    9869    11868   1       130
chr1    10010   12009   1       134
chr1    17437   19436   244     298

Command with -L option:

$wgbstools test_bimodal -L test.bed.gz sample.pat.gz

No results returned

Command with -r option for comparison:

$wgbstools test_bimodal -r chr1:9869-11868 sample.pat.gz

Results:

LL: -7.578929530800584 | 3 reads | 66 observed | BPI: 0.9236031051597491
LL: -10.5789295308006 | 3 reads | 66 observed | BPI: 0.8950005801519093
pvalue: 1.000e+00

Any ideas?

[yonniejon]

Hi!
Sorry about that. That is a problem with the documentation as it is not clear. test_bimodal using a bed file as input only prints out those regions which show statistically significant bimodal methylation (after FDR correction). It prints the bed file region and the corrected p-value. This should be documented and I will make a fix for this. Besides that I can add an option to print the p-value of all regions, and not just those which are bimodal.

[emblake85]

Thanks for clarifying! Is the corrected p-value threshold 0.05? It would be great to get the p-value for all regions in the bed file, not just significant regions - thanks!