diff --git a/analyses/focal-cn-file-preparation/02-add-ploidy-consensus.Rmd b/analyses/focal-cn-file-preparation/02-add-ploidy-consensus.Rmd index 7dc1733e25..86c26c789f 100644 --- a/analyses/focal-cn-file-preparation/02-add-ploidy-consensus.Rmd +++ b/analyses/focal-cn-file-preparation/02-add-ploidy-consensus.Rmd @@ -41,9 +41,7 @@ if(!dir.exists(output_dir)) { ``` ```{r} -# TODO: the consensus SEG file is not currently in the data download -- when it -# gets included we will have to change the file path here -consensus_seg_file <- file.path("..", "copy_number_consensus_call", "results", +consensus_seg_file <- file.path("..", "..", "data", "pbta-cnv-consensus.seg.gz") histologies_file <- file.path("..", "..", "data", "pbta-histologies.tsv")