exposure_differential_analysis: Compare exposures of annotated samples

In campbio/musicatk: Mutational Signature Comprehensive Analysis Toolkit

Compare exposures of annotated samples

Description

exposure_differential_analysis is used to run differential analysis on the signature exposures of annotated samples.

Usage

exposure_differential_analysis(
  musica,
  model_name,
  annotation,
  modality = "SBS96",
  result_name = "result",
  method = c("wilcox", "kruskal", "glm.nb"),
  group1 = NULL,
  group2 = NULL,
  ...
)

Arguments

musica	A musica object.
model_name	The name of the model.
annotation	Column in the sample_annotations table of the musica object
modality	The modality. Must be "SBS96", "DBS78", or "IND83". Default "SBS96".
result_name	Name of the result list entry. Default "result".
method	Any method in c("wilcox", "kruskal", "glm.nb") used to perform differential analysis on signature exposures
group1	character vector used in the Wilcox test. Elements in group1 are compared to elements in group2. This is required for annotation with more than 2 levels.
group2	character vector used in the Wilcox test. Elements in group2 are compared to elements in group1. This is required for annotation with more than 2 levels.
...	Additional arguments to be passed to the chosen method

Value

A matrix containing statistics summarizing the analysis dependent on the chosen method

Examples

data("res_annot")
exposure_differential_analysis(res_annot,
  model_name = "res_annot",
  annotation = "Tumor_Subtypes", method = "wilcox"
)

campbio/musicatk documentation built on Dec. 25, 2024, 9:34 p.m.