read_exposure {mSigTools}

Read an exposure matrix from a file.

Description

Read an exposure matrix from a file.

Usage

read_exposure(file, check.names = FALSE)

Arguments

file

File path to a CSV file containing an exposure matrix, i.e. the numbers of mutations due to each mutational signature. Each row corresponds to a mutational signature an each column corresponds to a tumor or other biological sample.

check.names

Passed to read.csv. IMPORTANT: If TRUE this will replace the double colon in identifiers of the form <tumor_type>::<sample_id> with two periods (i.e. <tumor_type>..<sample_id>. If check.names is true, generate a warning if double colons were present.

Value

Numerical matrix of exposures, with the same shape as the contents of file.

Examples

file <- system.file("extdata",
  "Liver-HCC.exposure.csv",
  package = "mSigTools"
)
exposure <- read_exposure(file)