find_mutations: Mutation Analysis Related to Signature Scores

In IOBR/IOBR: Immune Oncology Biological Research

Mutation Analysis Related to Signature Scores

Description

This function searches for mutations related to a specific signature score and conducts statistical tests to evaluate their significance. It can generate oncoprints and box plots to visualize the relationships and save the results.

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",
  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 with sample names in the rows and genes in the columns representing mutation data.
signature_matrix	A dataframe with identifier and target signatures.
id_signature_matrix	The column name in the signature_matrix that acts as the identifier.
signature	The name of the target signature for analysis.
min_mut_freq	The minimum frequency of mutations required to consider a gene in the analysis.
plot	A logical value; if TRUE, results will be plotted and saved at 'save_path'.
method	Specifies the statistical test method; "multi" for both Cuzick and Wilcoxon tests or "Wilcoxon" for only the Wilcoxon test.
save_path	The directory path where plots and statistical analysis results will be saved.
palette	The color palette for box plots.
show_plot	A logical variable; if TRUE, plots will be rendered on display.
show_col	Whether to show the color code of the palette.
width	The width of the oncoprint plot.
height	The height of the oncoprint plot.
oncoprint_group_by	Specifies how to group the oncoprint, options are "mean" or "quantile".
oncoprint_col	The color for mutations in the oncoprint.
gene_counts	The number of genes to display in the oncoprint.
jitter	A logical value; if TRUE, adds jitter to the box plot points.
genes	A vector of gene names for drawing; if NULL, genes are selected based on mutation frequency.
point_size	The size of points in the box plot.
point_alpha	The transparency level of points in the box plot.

Value

Returns a list containing results from the statistical tests, oncoprint plots, and box plots.

Author(s)

Dongqiang Zeng

Examples

# Load mutation and signature data
maf_file <- "path_to_maf_file"
mut_list <- make_mut_matrix(maf = maf_file, isTCGA = TRUE, category = "multi")
mut <- mut_list$snp
# Assume 'tcga_stad_sig' is preloaded with appropriate data
results <- find_mutations(mutation_matrix = mut, signature_matrix = tcga_stad_sig,
                          id_signature_matrix = "ID", signature = "CD_8_T_effector",
                          min_mut_freq = 0.01, plot = TRUE, method = "multi",
                          save_path = "path_to_save_results")

IOBR/IOBR documentation built on Sept. 9, 2024, 8:36 p.m.