extract_tmb: #' Extract total mutation burden (TMB) of tumors in a maf...

In c7rishi/hidgenclassifier: Functions for Bayesian hierarchical hidden genome classifier

#' Extract total mutation burden (TMB) of tumors in a maf file

Description

#' Extract total mutation burden (TMB) of tumors in a maf file

Usage

extract_tmb(maf, variant_col = "variant", sample_id_col = "sample", ...)

Arguments

maf	mutation annotation file – a data frame-like object with at least two columns containing variant labels and sample IDs. NOTE: uniqueness of rows of maf is assumed.
variant_col	name of the column in maf containing variant labels.
sample_id_col	name of the column in maf containing tumor sample IDs.
...	Unused.

Value

Returns a numeric vector providing the total number of mutations observed in each tumor in maf, named by the sample ids in maf.

Examples

data("impact")
tmb <- extract_tmb(
  maf = impact,
  variant_col = "Variant",
  sample_id_col = "patient_id"
)
tmb

c7rishi/hidgenclassifier documentation built on June 14, 2024, 11:10 a.m.