Man pages for kgori/sigfit
Flexible Bayesian inference of mutational signatures

build_cataloguesBuild mutational catalogues
build_opps_matrixBuild a opportunities matrix
convert_signaturesConvert signatures between models
cosine_simCosine similarity between two vectors
cosmic_signatures_v3Single base substitution signatures from COSMIC v3
cosmic_signatures_v3_strandSingle base substitution signatures from COSMIC v3 with...
default_sig_paletteGenerate default colour palette for signatures
extract_signaturesExtract signatures from a set of mutation counts
extract_signatures_initialiserUse optimization to generate initial parameter values for...
fetch_cosmic_dataFetch COSMIC mutational signatures
fit_extract_signaturesFit-and-extract mutational signatures
fit_signaturesFit mutational signatures
get_loglikGenerate log likelihood values from a model
get_reconstructionsGenerate reconstructed mutation catalogues from parameters...
human_trinuc_freqsRetrieve human trinucleotide frequencies
l2_normL2 norm between two vectors
letterwrapFrom Produce...
make_colorsColour warnings for posterior predictive checks yellow =...
match_signaturesFind the best matches between two sets of signatures
mut_typesGenerates character vector of 96 (or 192, if strand=TRUE)...
plot_allPlot all results from signature fitting or extraction
plot_exposuresPlot signature exposures
plot_gofPlot goodness of fit
plot_ppcPlot result of posterior predictive check black = observed...
plot_reconstructionPlot mutational spectrum reconstructions
plot_spectrumPlot mutational spectra
remove_zeros_Deal with zero values in a signature
retrieve_parsRetrieve model parameters
rev_compReverse complement a nucleotide sequence string Input is...
sigfit-packageThe 'sigfit' package.
simulate_ppcGenerate posterior predictive check values from a model
stan_modelsAccess stan models
to_matrixInitial coercion to matrix for signatures/exposures/counts
kgori/sigfit documentation built on Aug. 9, 2019, 3:28 p.m.