COSMIC_signatures_corr: Calculate cosine similarity of mutational signature with...

Description Usage Arguments

View source: R/COSMIC_signatures_corr.R

Description

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

Usage

1
COSMIC_signatures_corr(mutational_processes_file, plot=FALSE, outfile, cutoff=0.7, annot_outfile, ...)

Arguments

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.


lixiangchun/lxctk documentation built on May 21, 2019, 6:44 a.m.