Compare exposures of annotated samples — exposure_differential

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"
)
#>    Signature Group1 Group2          Pr(>|z|)             (fdr)
#> 1 Signature1 Breast   Lung 0.114285714285714 0.342857142857143
#> 2 Signature2 Breast   Lung 0.228571428571429 0.342857142857143
#> 3 Signature3 Breast   Lung 0.628571428571429 0.628571428571429