Open JMarzec opened 2 weeks ago
I run RNAsum using the “full” and "partial" TCGA patients reference cohort options for the following samples:
SBJ04426 BRCA SBJ04187 BRCA SBJ04296 BRCA SBJ01649 PANCAN SBJ04469 PANCAN SBJ02061 PANCAN SBJ02091 PANCAN SBJ04376 PANCAN SBJ04408 PANCAN
Attached are summary plots illustrating the following:
Based on the "RNAsum processing time by chunk" chart , the following R code chunks are the most computationally demanding (comments in "()" indicate whether respective chunks can be skipped using the "full" TCGA reference option):
(can be skipped) data_transformation_plot (keep) glance_expr_plot_immune_genes (keep) pca (keep) glance_expr_plot_cancer_genes (can be skipped) data_transformation_display (keep) glance_expr_plot_hrd_genes (keep) top_hits_fusions (keep) unnamed-chunk-1 (keep) rle
I'd also skip "data_normalisation_plot", "scree_combined_data_display" and "rle_display" chunks since these are not readable given the number of included samples.
Consider the following matters to address when adding the option to use the “full” TCGA patients reference cohort