COSMIC_signatures_corr: Calculate cosine similarity of mutational signature with...
In lixiangchun/lxctk: Li Xiangchun's tool-kit (lxctk)

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 `decipherMutationalSignatures` pipeline.
`plot`	If TRUE, visualize similarity with a heatmap.
`outfile`	If provided, similarity result is exported to `outfile`.
`cutoff`	Cutoff of cosine similarity for downstream annotation.
`annot_outfile`	If provided, annotation against Alexandrov et al. is written to `annot_outfile`.
`...`	Additional params passed to `NMF::aheatmap`.