jharenza
commented
2 years ago @runjin326 - #1189 creates N per cancer group tables. Will you pick up the remaining:
- table of N per oncoprint including not shown/not mutated samples (N for samples in HGAT oncoprint, embryonal oncoprint, etc) and the below, which I forgot to write above:
- export table of gene with number of mutated samples per oncoprint (for ex, in LGAT, how many samples have BRAF mutations? The percents are in the oncoprint, but would also like to write the Ns)
runjin326
What analysis module should be updated and why?
oncoprint-landscape
In writing the manuscript, I need to reference the Ns per group when listing out frequencies, so I think we should either have some output table with this info or an update in the readme - probably easier to do the former in case of any changes.
What changes need to be made? Please provide enough detail for another participant to make the update.
Would be ideal to create a table or notebook with N per total samples listed in A,B,C,D and then Ns per each cancer group.
Also note, there are a lot of samples which are not shown in the oncoprint because they lack mutations, but they should be included in the total N since they are included in the denominator of the frequency.
What input data should be used? Which data were used in the version being updated?
primary sample list only, v21
When do you expect the revised analysis will be completed?
?
Who will complete the updated analysis?
@cbethell ?@kgaonkar6 cc @jaclyn-taroni