calPropDriver: calPropDriver calculates the proportions of driver mutation...

In qingjian1991/MPTevol: Clonal Evolutionary History and Metastatic Routines Analysis for Multiple Primary Tumors

calPropDriver calculates the proportions of driver mutation for mutation sets.

Description

The mutations are classified by classifyMut() internally.

Usage

calPropDriver(
  maf,
  patient.id = NULL,
  driverGene,
  class = "SP",
  classByTumor = FALSE,
  vaf.cutoff = 0.01,
  silent.columns = NULL
)

Arguments

maf	Maf or MafList object generated by readMaf() function
patient.id	Select the specific patients. Default NULL, all patients are included.
driverGene	The driver Gene names (Genes Symbols)
class	The class which would be represented. "SP" (Shared pattern: Public/Shared/Private), other options: "CS" (Clonal status: Clonal/Subclonl) and "SPCS". see MesKit::classifyMut().
classByTumor	Logical (Default: FALSE). Classify mutations based on "Tumor_ID".
vaf.cutoff	Removing mutations of low variant allele frequency (VAF).
silent.columns	The Variant_Classification field in the MAF files that indicates the silent mutations. Defaults: c("Silent", "3'Flank", "IGR", "Intron", "RNA")

Examples

# Get the driver gene.
driverGene <- read.delim(system.file(package = "MPTevol", "extdata", "IntOGen-Drivers-Cancer_Genes.tsv"), header = T) %>%
filter(CANCER_TYPE %in% c("BRCA", "COREAD", "LUAD", "LUSC")) %>%
  pull(SYMBOL) %>%
  unique()

prop = calPropDriver(maf, patient.id = "BRCA", driverGene = driverGene)

prop$BRCA$plot

qingjian1991/MPTevol documentation built on Jan. 30, 2023, 10:16 p.m.