View source: R/COSMIC_signatures_corr.R
Calculate cosine similarity of mutational signature with those reported by Alexandrov et al. The update signature probabilities was downloaded from http://cancer.sanger.ac.uk/cosmic/signatures on 2016-07-30.
wget http://cancer.sanger.ac.uk/cancergenome/assets/signatures_probabilities.txt
1 | COSMIC_signatures_corr(mutational_processes_file, plot=FALSE, outfile, cutoff=0.7, annot_outfile, ...)
|
mutational_processes_file |
Mutational processes file obtained from |
plot |
If TRUE, visualize similarity with a heatmap. |
outfile |
If provided, similarity result is exported to |
cutoff |
Cutoff of cosine similarity for downstream annotation. |
annot_outfile |
If provided, annotation against Alexandrov et al. is written to |
... |
Additional params passed to |
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