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CompSign: An R package for differential abundance of compositional mutational signatures

Lena Morrill Gavarró 2024

You can install the package as follows:

library(devtools)
devtools::install_github("lm687/CompSign", build_vignettes = TRUE)

Several examples of input data, how to run the models, and how to interpret the results are found in the vignette:

browseVignettes("CompSign")

This package as, applied to study the differences in mutational signatures between clonal and subclonal mutations in the PCAWG dataset. The github repository reproducing these results can be found here.

We refer to the vignettes for a more in-depth explanation of models and the functioning of the package, but a minimal example is found here:

The function wrapper_run_TMB() is used to run all variations of the model.

The input dataset is the argument object, which is a list with the following structure:

• x: covariate matrix (p x n)
• z: matrix of random effects indicating which patient-specific subsample belongs to which patient (n x N)
• Y (n x d)
• d

A minimal example is:

diagDM_no_small_sigs <- wrapper_run_TMB(object = simplified_object,
                                        model = "diagREDM", use_nlminb=T, smart_init_vals=F)

in which simplified_object is a list containing simplified_object$x, simplified_object$z, simplified_object$Y, simplified_object$d.

The first row is the <model> argument in the function wrapper_run_TMB().