load_PCAWG: Function to load an exposures object

In lm687/CompSign: Study of mutational signatures using compositional data analysis (CoDA) techniques

Function to load an exposures object

Description

Function to load an exposures object

Usage

load_PCAWG(
  ct,
  typedata,
  simulation = FALSE,
  path_to_data = "../../data/",
  read_directly = FALSE,
  old_version_creating_X_Z = F,
  load_all_sigs = F,
  override_warning_X_Z = F
)

Arguments

ct:	cancer type, if the data are organised as in the PCAWG dataset. Otherwise, name of ile
typedata:	type of data (simulation/nucleotidesubstitution1/nucleotidesubstitution3/signatures/etc.), if the data are organised as in the PCAWG dataset
simulation:	boolean indicating if the data are simulations (i.e. not organised as in the PCAWG dataset)
path_to_data:	path to folder which includes the file to upload
read_directly:	boolean indicating if <ct> includes the filename
old_version_creating_X_Z:	boolean indicating if the input file contains exposures organised as in <<Display A>>
load_all_sigs:	load all signatures (otherwise, only active signatures are loaded)
override_warning_X_Z:	allow X and Z to be generated assuming that the input file contains exposures organised as in <<Display A>>

Value

the covariance matrix get the first element of the list, because the second is the set of the parameters used in the creation of the dataset

lm687/CompSign documentation built on Feb. 1, 2024, 4:41 p.m.