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GENOME-MUSIC-SMG(1p) User Contributed Perl Documentation GENOME-MUSIC-SMG(1p)

genome music smg


genome music smg - Identify significantly mutated genes.


This document describes genome music smg version 0.04 (2018-07-05 at 09:17:13)


genome music smg --gene-mr-file=? --output-file=? [--max-fdr=?] [--skip-low-mr-genes] [--bmr-modifier-file=?] [--processors=?]

 ... music smg \
      --gene-mr-file output_dir/gene_mrs \
      --output-file output_dir/smgs

(A "gene-mr-file" can be generated using the tool "music bmr calc-bmr".)


File with per-gene mutation rates (Created using "music bmr calc-bmr")
Output file that will list significantly mutated genes and their p-values


The maximum allowed false discovery rate for a gene to be considered an SMG

Default value '0.2' if not specified

Skip testing genes with MRs lower than the background MR

Default value 'true' if not specified

Make skip-low-mr-genes 'false'
Tab delimited multipliers per gene that modify BMR before testing [gene_name bmr_modifier]
Number of processors to use (requires 'foreach' and 'doMC' R packages)

Default value '1' if not specified


This script runs R-based statistical tools to identify Significantly Mutated Genes (SMGs), when given per-gene mutation rates categorized by mutation type, and the overall background mutation rates (BMRs) for each of those categories (gene_mr_file, created using "music bmr calc-bmr").

P-values and false discovery rates (FDRs) for each gene in gene_mr_file is calculated using three tests: Fisher's Combined P-value test (FCPT), Likelihood Ratio test (LRT), and the Convolution test (CT). For a gene, if its FDR for at least 2 of these tests is <= max_fdr, it will be output as an SMG. Another output file with prefix "_detailed" will have p-values and FDRs for all genes.



 Qunyuan Zhang, Ph.D.
 Cyriac Kandoth, Ph.D.
 Nathan D. Dees, Ph.D.
2018-07-05 perl v5.26.2