facets.dat: facets.dat

In margarethannum/gnomeR: What the Package Does (One Line, Title Case)

Description

Creates a copy number alteration matrix from segment files.

Usage

facets.dat(seg = NULL, filenames = NULL, path = NULL,
  patients = NULL, min.purity = 0.3, epsilon = 0.005, adaptive = F)

Arguments

seg	a segmentation file containing the segmentation information of multiple patients
filenames	the names of the segment files to be loaded and processed (Note must end in ".Rdata").
path	the relative path to the files folder from your current directory
patients	the names of the patients of the respective filenames. Default simply 1 to number of files.
min.purity	the minimum purity of the sample required to be kept in the final dataset. Default is 0.3.
epsilon	level of unions when aggregating segments between

Value

out.cn : a matrix of the union of all segment files with patients as rows and segments as columns

ploidy : a vector of the ploidy values for the patients in out.cn

purity : a vector of the purity values for the patients in out.cn

FGAs : a vector of the fragment of genome altered values for the patients in out.cn

Examples

library(gnomeR)

margarethannum/gnomeR documentation built on Feb. 26, 2020, 8:16 p.m.