CombineChainsAndExtractSigs: Extract signatures etc. from multiple Gibbs sample chains

In steverozen/mSigHdp: Mutational signature discovery using HDP (hierarchical Dirichlet process)

Extract signatures etc. from multiple Gibbs sample chains

Description

Extract signatures etc. from multiple Gibbs sample chains

Usage

CombineChainsAndExtractSigs(
  clean.chlist,
  input.catalog,
  verbose = FALSE,
  high.confidence.prop = 0.9,
  merge.raw.cluster.args = hdpx::default_merge_raw_cluster_args()
)

Arguments

clean.chlist	A list of hdpSampleChain-class S4 objects, each with the information from one Gibbs sampling chain. See hdpSampleChain-class in package hdpx.
input.catalog	Input spectra catalog as a matrix.
verbose	If TRUE then message progress information.
high.confidence.prop	Raw clusters of mutations found in >= high.confidence.prop proportion of posterior samples are signatures with high confidence.
merge.raw.cluster.args	See default_merge_raw_cluster_args in package hdpx.

Value

Invisibly, a list with the following elements:

signature

The extracted signature profiles as a matrix; rows are mutation types, columns are signatures with high confidence.

signature.post.samp.number

A data frame with two columns. The first column corresponds to each signature in signature and the second columns contains the number of posterior samples that found the raw clusters contributing to the signature.

signature.cdc

A numeric data frame. Columns correspond to signatures as in signature. Rows correspond to either biological samples or to parent and grandparent Dirichlet processes.

exposureProbs

The inferred exposures as a matrix of mutation probabilities; rows are signatures, columns are samples (e.g. tumors). This is similar to signature.cdc, but every column was normalized to sum to 1.

low.confidence.signature

The profiles of signatures extracted with low confidence as a matrix; rows are mutation types, columns are signatures with < high.confidence.prop of posterior samples.

low.confidence.post.samp.number

Analogous to signature.post.samp.number, except that this one is for signatures in low.confidence.signature.

low.confidence.cdc

Analogous to signature.cdc, except that columns in this matrix correspond to columns in low.confidence.signature.

extracted.retval

A list object returned from extract_components in package hdpx.

steverozen/mSigHdp documentation built on Feb. 6, 2023, 1:36 a.m.