Petr Smirnov

Git PAT token not used when installing packages?

11

I am experiencing the known issue with autoscale and github package installation, where the error message is: ``` Error: HTTP error 403. API rate limit exceeded for 52.*******. (But here's...

For microarray data (or any data really), we would like to be able to summarize rows of molecular data by a user provided function (mean/median or a custom function), based...

What to do with PharmacoGx:::.summarizeSensitivityNumbers

1

PharmacoGx:::.summarizeSensitivityNumbers, or equivalently the table returned by sensNumbers is sometimes a slight misrepresentation of the actual data available in Profiles, due to various QC filters which will keep an experiment...

Check on wrong assay?

3

https://github.com/bhklab/PharmacoGx/blob/eeee68a021549bdfab23e85cdf57c15ae54a52cc/R/methods-summarizeMolecularProfiles.R#L227 Im about 60% sure this is supposed to be a 2 in the if statement, it does not really make much sense otherwise. The first assay should not be...

InterectPSets still doesnt do the right thing on concentrations?

1

When cell lines and drugs are not both selected in addition to concentrations, the concentrations intersection is skipped it seems. Need to verify. In addition, intersection small example datasets on...

sensitivity.cutoff

2

@zhaleh-safikhani: Can you check the drugSensSig function? The documentation for the sensitivity.cutoff feature says it is used as a filter for values out of range, but the actual line being...

check new unionist implementation to handle NAs