facets.heatmap: facets.heatmap

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

Description

Creates a heatmap of copy number profiles from segment files.

Usage

facets.heatmap(seg = NULL, filenames = NULL, path = NULL,
  patients = NULL, min.purity = 0.3, epsilon = 0.005,
  ordered = NULL, outcome = NULL, 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
ordered	order in which patients should be printed. Default NUll leads to hierarchical clustering.
outcome	for seg file only, if outcome associated with study it will be printed along the x axis for each patient

Value

p a heatmap corresponding to the segnment files inputted

Examples

library(gnomeR)

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