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mSigTools

Purpose

Utility functions for mutational signature analysis.

Installation

Get the latest released version

if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}
remotes::install_github(repo = "Rozen-Lab/mSigTools")

Get the development version

Install mSigTools from the master branch on GitHub:

if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}
remotes::install_github(repo = "Rozen-Lab/mSigTools", ref = "master")

Reference manual

https://github.com/Rozen-Lab/mSigTools/blob/v1.0.7-branch/mSigTools_1.0.7.pdf

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Version

Install

install.packages('mSigTools')

Monthly Downloads

179

Version

1.0.7

License

GPL-3

Issues

0

Pull Requests

0

Stars

2

Forks

2

Maintainer

Steven Rozen

Last Published

January 13th, 2023

Functions in mSigTools (1.0.7)

write_exposure

Write an exposure matrix to a file.
match_two_sig_sets

Find an optimal matching between two sets of signatures subject to a maximum distance.
plot_exposure

Plot exposures in multiple plots, with each plot showing exposures for a manageable number of samples.
optimize_exposure_QP

Quadratic programming optimization of signature activities
plot_exposure_to_pdf

Plot exposures in multiple plots to a single PDF file, with each plot showing exposures for a manageable number of samples.
TP_FP_FN_avg_sim

Find best matches (by cosine similarity) of a set of mutational signatures to a set of reference mutational signatures.
read_exposure

Read an exposure matrix from a file.
sort_exposure

Sort columns of an exposure matrix based on the number of mutations in each sample (column).
plot_exposure_internal

Plot a matrix of exposures in a single plot.
find_best_reconstruction_QP

Find "best" reconstruction of a target signature or spectrum from a set of signatures.
sig_dist_matrix

Compute a matrix of distances / similarities between two sets of signatures.