confidenceSig: Provides interval of uncertainty for estimated weights of...

Description Usage Arguments Details Value See Also Examples

View source: R/confidenceSig.R

Description

Provides an interval of uncertainty for estimated weights of known mutation signatures in the catalog of mutations from a set of samples.

Usage

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confidenceSig(contextfreq.sample, subsample=0.8, iter=1000 , signatures.ref=signatures.cosmic, lbound=0.1, ubound=0.9, replace=FALSE)

Arguments

contextfreq.sample

A sample from the dataframe of class contextfreq containing mutation frequency in trinucleotide contexts.

subsample

Proportion of mutations included during each subsampling. Default: 0.8 (80 percent)

iter

Number of iterations of subsampling. Default: 1000

signatures.ref

An object of class mutsig comprising the set of signatures. (signatures.nature2013 or signatures.cosmic or signatures.cosmic.2019 ), Default: 'signatures.cosmic'

lbound

Lower bound of the interval of uncertainty for estimated weights of the signatures Default: 0.1 (10 percent)

ubound

Upper bound of the interval of uncertainty for estimated weights of the signatures Default: 0.9 (90 percent)

replace

should sampling be with replacement? TRUE or FALSE

Details

Provides an interval of uncertainty for estimated weights of known mutation signatures in the catalog of mutations from a set of samples. First, based on the catalog of mutations in a sample, weights of the mutation signatures are estimated. Next, mutations are subsampled iteratively without replacement, each time estimating the weights of the mutation signatures. The intervals of uncertainty for weights of each mutation signatures are determined by aggregating observations from a given number of iterations.

Value

An object containing the following information:

  1. observed.weights: A data frame containing estimated weights of known mutation signatures based on all mutations in a sample.

  2. median.weights: A data frame containing estimated median of the weights of known mutation signatures based on iteratively subsampled mutations.

  3. ubound.weights: A data frame containing upper-bound values of the weights of known mutation signatures based on iteratively subsampled mutations.

  4. lbound.weights: A data frame containing lower-bound values of the weights of known mutation signatures based on iteratively subsampled mutations.

See Also

Examples

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data(contextfreq.sample_test)
robust_sig_object=confidenceSig(contextfreq.sample=contextfreq.sample_test[1,], subsample=0.8, 
iter=50, signatures.ref=signatures.cosmic, lbound=0.1, ubound=0.9, replace=FALSE)

sjdlabgroup/MutSigTools documentation built on Oct. 5, 2019, 3:31 a.m.