README.md

In lm687/CompSign: Study of mutational signatures using compositional data analysis (CoDA) techniques

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

Lena Morrill Gavarró 2024

Installation

You can install the package as follows:

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

Vignette

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.

Brief summary of the package

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:

How to run the model

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

Input dataset

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

Estimating the parameters

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.

Variations of the model

The first row is the <model> argument in the function wrapper_run_TMB(). | name of model (for user) | description |cpp file (no need to use) | |---|---|---| | diagREDMsinglelambda | DM with independent RE and one lambda | diagRE_dirichletmultinomial_single_lambda | | diagRE_DM | DM with independent RE and two lambdas | diagRE_ME_dirichletmultinomial | | diagRE_M | M with independent RE | diagRE_ME_multinomial | | FEDMsinglelambda | DM with no RE and one lambda | FE_dirichletmultinomial_single_lambda | | FE_DM | DM with no RE and two lambdas | FE_dirichletmultinomial | | fullREDMsinglelambda | DM with independent RE and two lambdas | fullRE_dirichletmultinomial_single_lambda | | fullRE_DMonefixedlambda | DM assuming that there is no overdispersion in the first group (fixed lambda=1) | fullRE_ME_dirichletmultinomial_onefixedlambda | | fullRE_DM | DM with correlated RE and two lambdas | fullRE_ME_dirichletmultinomial | | fullRE_M | M with correlated RE | fullRE_ME_multinomial | | singleRE_DM | DM with a single RE intercept and two lambdas | singleRE_dirichlet_multinomial | | diagDMpatientlambda | DM with independent RE and one lambda for each patient | diagREpatientlambda_ME_dirichletmultinomial | | fullDMpatientlambda | DM with correlated RE and one lambda for each patient | fullREpatientlambda_ME_dirichletmultinomial |

lm687/CompSign documentation built on Feb. 1, 2024, 4:41 p.m.