find_mutations: Searching for mutations related to signature score

In IOBR/IOBR: Immune Oncology Biological Research

Searching for mutations related to signature score

Description

Searching for mutations related to signature score

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	mutation matrix with sample name in the row and genes in the column
signature_matrix	signature data frame with identifier and target signatures
id_signature_matrix	column name of identifier
signature	name of target signature
min_mut_freq	minimum frequency of mutations
plot	logical variable, if TRUE, plot will be save in the 'save_path'
method	multi or Wilcoxon test only, if 'multi' is applied, both 'cuzick test' and 'wilcoxon' will be performed
point.alpha	point.alpha of boxplot
save_path	path to save plot and statistical analyses
palette	palette of box plot
show_plot	logical variable, if TRUE, plot will be printed.
show_col	show code of palette
width	width of oncoprint
height	height of oncoprint
oncoprint_group_by	signature must be group by mean or quantile
oncoprint_col	color of mutation
gene_counts	define the number of genes which will be shown in the oncoprint
jitter	if true, each point will be drawn in the box plot with jitter
genes	genes for drawing
point_size	default is 4.5

Author(s)

Dongqiang Zeng

Examples

# MAF data download from UCSC Xena hub
maf_file<-"E:/18-Github/Organization/TCGA.STAD.mutect.c06465a3-50e7-46f7-b2dd-7bd654ca206b.DR-10.0.somatic.maf"
mut_list<-make_mut_matrix(maf = maf_file, isTCGA   = T, category = "multi")
mut<-mut_list$snp
res<-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, jitter = TRUE, point.alpha = 0.25

IOBR/IOBR documentation built on May 5, 2024, 2:34 p.m.