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