quickSig: quickSig

In mskilab/skitools: Various mskilab R utilties

quickSig

Description

Quick implementation of Mike / Gaddy binomial / poisson model. Requires category based coverage output (*.per_gene.coverage.txt file) computed during mutsig preprocess step. (run mutsig_preprocess setting the following additional flags: P.output_per_gene_coverage = true; P.output_per_gene_mutation_counts = true; P.simplified_gene_sample_coverage_table = false; P.simplified_gene_sample_mutation_counts_table = false; )

Computes context-category specific mutation rates either across whole cohort or within strata of gene-patient categories.

Outputs a significance table with the following columns for each category (if analyze.categories = TRUE) and/or category "tot" which is across all categories o.k = observed mutations of category k e.k = expected mutations of category k given background model eff.k = log(o.k / e.k) for category k p.k = p value of deviation from expectation under poisson model q.k = q value of deviation

Usage

quickSig(
  maf,
  cov,
  patients = NULL,
  genes = NULL,
  analyze.categories = F,
  remove.silent = TRUE,
  limit.cat = NULL,
  two.tailed = TRUE
)

Author(s)

Marcin Imielinski

mskilab/skitools documentation built on Aug. 31, 2023, 1:13 p.m.