Man pages for eyzhao/SignIT
Mutation signatures in individual tumours

all_snv_mutation_typesGets a list of the standard 96 mutation types used in SNV...
base_complementReturns the complementary sequence for a set of strings
collapse_mutation_typesCollapses mutation types of G>N and A>N mutations into C>N...
compute_population_bicBayesian Information Criterion for Population Models
compute_population_model_log_likelihoodLog Likelihood of Population Model
compute_population_signatures_bicBayesian Information Criterion for Population Signatures
compute_population_signatures_log_likelihoodLog Likelihood of Population Signatures Model
compute_population_signatures_waicWatanabe-Akaike Information Criterion for Population...
compute_signatures_waicWatanabe-Akaike Information Criterion for Signatures
get_density_modeConvenience function for estimating the mode of dataset's...
get_exposure_pairwise_correlationsPairwise correlation coefficients between signatures
get_exposuresCompute the MCMC sample space of exposure vectors
get_exposure_summary_tableCreates a summary table of exposure statistics
get_osGets the OS name
get_population_parameter_estimatesPoint estimates for population Stan model output
get_populationsSignIT population model without mutation signatures
get_population_signaturesSignIT-Pop inference of populations and signatures
get_reference_signaturesRetrieves built-in reference mutation signature sets
get_signature_bleed_graphGraph Representing Signature Bleed Relationships
get_signature_namesParse Signature Names from Reference Signatures
get_snv_mutation_typeGiven chromosome, position, reference, and altered allele...
get_trinucleotideGets the trinucleotide context for a set of genomic...
get_vaf_correctionComputes the VAF correction factor for a table of mutations
map_phi_to_populationPopulation Index Mapper
map_phi_to_signatureSignature Index Mapper
map_population_signaturesMaps Population Signature Parameters to their Signatures and...
mcmc_exposures_as_matrixMCMC Exposures to Matrix
mutations_to_catalogGiven chromosome, position, reference, and altered allele...
mutation_types_matchCheck Whether Mutation Types Match
normalize_reference_signaturesNormalization of reference signatures.
parse_stan_outputStan Output Parser
plot_bleed_interactionsCreates a circular plot with links between signatures that...
plot_exposure_chainPlot the MCMC chains for the signature exposure solutions
plot_exposure_posteriorsPlot the signature exposure posterior distributions
plot_exposure_posteriors_bleedPlot the signature exposure posterior distribution along with...
plot_nnls_solutionPlots a simple NNLS solution
plot_population_signaturesPlot Population Signatures
plot_signature_pairwise_bleedPlots pairwise correlations between signatures in MCMC...
plot_two_signature_hexplotPlots a hexplot between two signatures
reference_signatures_as_matrixConvert reference signatures to matrix
reverse_factor_levelsReverse Factor Levels
reverse_factor_ranksReverse Factor Ranks
rotate_x_axis_labelsRotates the x axis labels 90 degrees in ggplot graphs.
select_n_populationsAutomatic Model Selection for Number of Populations
signit-packageSignIT: Mutation Signatures in Individual Tumours
stitch_mutation_typesGiven a set of substitutions and trinucleotides, merge into...
subset_reference_signaturesAutomatic subsetting of reference mutation signatures
summarise_population_signaturesSummarise Population Signatures
trim_signature_namesTrims the names of mutation signatures
eyzhao/SignIT documentation built on Aug. 29, 2018, 6:53 a.m.