find_mutations: Analyze Mutations Related to Signature Scores

In IOBR: Immune Oncology Biological Research

Analyze Mutations Related to Signature Scores

Description

This function identifies mutations associated with a specific signature score, performs statistical tests for significance, and generates oncoprints and box plots to visualize relationships.

Usage

find_mutations(
  mutation_matrix,
  signature_matrix,
  id_signature_matrix = "ID",
  signature,
  min_mut_freq = 0.05,
  plot = TRUE,
  method = "multi",
  point_alpha = 0.1,
  save_path = NULL,
  palette = "jco",
  cols = NULL,
  show_plot = TRUE,
  show_col = FALSE,
  width = 8,
  height = 4,
  oncoprint_group_by = "mean",
  oncoprint_col = "#224444",
  gene_counts = 10,
  jitter = FALSE,
  genes = NULL,
  point_size = 4.5
)

Arguments

mutation_matrix	A matrix of mutation data with samples in rows and genes in columns.
signature_matrix	A data frame with sample identifiers and signature scores.
id_signature_matrix	Column name in 'signature_matrix' for sample identifiers.
signature	Name of the target signature for analysis.
min_mut_freq	Minimum mutation frequency required for gene inclusion. Default is 0.05.
plot	Logical indicating whether to generate and save plots. Default is TRUE.
method	Statistical test method: "multi" for both Cuzick and Wilcoxon, or "Wilcoxon" only. Default is "multi".
point_alpha	Transparency of points in box plot. Default is 0.1.
save_path	Directory to save plots and results. If NULL, no files are saved.
palette	Color palette for box plots(used when cols is NULL). Default is "jco".
cols	Character vector. Custom colors for box plots. If NULL, uses palette. Default is NULL.
show_plot	Logical indicating whether to display plots. Default is TRUE.
show_col	Logical indicating whether to show color codes. Default is FALSE.
width	Width of oncoprint plot. Default is 8.
height	Height of oncoprint plot. Default is 4.
oncoprint_group_by	Grouping method for oncoprint: "mean" or "quantile". Default is "mean".
oncoprint_col	Color for mutations in oncoprint. Default is "#224444".
gene_counts	Number of genes to display in oncoprint. Default is 10.
jitter	Logical indicating whether to add jitter to box plot points. Default is FALSE.
genes	Optional vector of gene names; if NULL, selects based on frequency.
point_size	Size of points in box plot. Default is 4.5.

Value

A list containing statistical test results, oncoprint plots, and box plots.

Author(s)

Dongqiang Zeng

Examples

## Not run: 
# This example requires a MAF file from TCGA or maftools
# See maftools or TCGAbiolinks documentation for obtaining MAF files
mut_list <- make_mut_matrix(
  maf = "path_to_maf_file", isTCGA = TRUE,
  category = "multi"
)
mut <- mut_list$snp
results <- find_mutations(
  mutation_matrix = mut, signature_matrix = signature_data,
  id_signature_matrix = "ID", signature = "CD_8_T_effector",
  min_mut_freq = 0.01, plot = TRUE, method = "multi"
)

## End(Not run)

IOBR documentation built on May 30, 2026, 5:07 p.m.