The internal call of assign_cn_to_ssm in comp_report.R calls GAMBLR.results exclusive parameters, causing issues when a non-GSC user runs this function with GAMBLR.data as their only way of retrieving data (i.e calling assign_cnm_to_ssm) (issue #8).
In fancy_propcov_plot, if the user does not provide a data frame with collated results (QC metrics) for comparison values the function inaccurately calls collate_qc_results, this has been updated to properly call collate_results instead.
Lingering issue with heatmap_mutation_frequency_bin.R that wrongly expects id_ease to return a list with metadata and sample IDs as its objects. This has been updated to behave in the expected way.
This PR addresses a few things:
assign_cn_to_ssmincomp_report.RcallsGAMBLR.resultsexclusive parameters, causing issues when a non-GSC user runs this function withGAMBLR.dataas their only way of retrieving data (i.e callingassign_cnm_to_ssm) (issue #8).fancy_propcov_plot, if the user does not provide a data frame with collated results (QC metrics) for comparison values the function inaccurately callscollate_qc_results, this has been updated to properly callcollate_resultsinstead.heatmap_mutation_frequency_bin.Rthat wrongly expectsid_easeto return a list with metadata and sample IDs as its objects. This has been updated to behave in the expected way.