Propose FDR on top of Bonferroni for multiple testing
With current version of ccqtl allowing for multiple phenotypes to be processed at once, need to allow to adjust for multiple testing: ajd arg of find_peaks script.
At present, ajd is yes/no and if yes performs Bonferroni adjustment, div by npheno, which may be (way) too conservative.
Todo: propose also FDR, which is more lenient. Steps:
-
check https://www.bioconductor.org/packages/release/bioc/html/qvalue.html package compatibility etc -
values taken by adj arg: none, Bonferroni, FDR (rather than yes/no)
Expected timeframe: next milestone, enhancement, not critical at all yet.