Clean Filter.R

[sync-by-unito]

on 8/16 Phil and Kelly discussed additional changes needed to clean up R/Filter.R script. Changes are denoted by TODO: in script with appropriate comments on work to be done

[kelly-sovacool]

grep -n TODO R/*

R/filter.R:122:  # TODO we should use "feature" instead of "gene" to make sure this is applicable beyond RNA-seq
R/filter.R:124:  # TODO: just have users specify hex values directly for simplicity
R/filter.R:159:  # TODO separate slots in S7 for samples, counts, annotations --> create function to validate
R/filter.R:181:  # TODO move this function call to the S7 validator
R/filter.R:314:#' TODO this function also transforms raw counts to CPM, but that should be a separate function before this step, before filter_counts function()
R/filter.R:315:#' TODO document `isexpr1` column in output
R/heatmap.R:14:    # TODO this only works on dataframes, not tibbles
R/rename.R:3:#' TODO this should happen right at the beginning of the template?
R/rename.R:5:#' TODO accept new names for samples in sample metadata spreadsheet
R/rename.R:9:#' @param samples_to_rename_manually TODO use sample metadata spreadsheet custom column
R/rename.R:18:    # TODO: refactor with dplyr::rename for simplicity