calculateInterfaceArea: Calculate total area and density of tumor interface

In caitlinjones/halo: Development version of the package 'halo', which analyzes and visualizes Halo data

Description

Calculate area and density of cells within a given distance to a tumor boundary

Usage

calculateInterfaceArea(dat, aFiles = NULL, haloAnnotations = NULL,
  writeCSVfiles = TRUE, maxG = 5, outDir = NULL,
  interfaceBins = (-36:36) * 10)

Arguments

aFiles	a vector of Halo boundary annotation files, with '.annotations' extension in XML format
writeCSVfiles	logical indicating whether to write density and area tables to file; default=TRUE
maxG	the maximum factor of 10 to use for generating random points for area calculation
outDir	if writeCSVfiles=T, directory to which these files will be written
interfaceBins	a vector of distances from tumor interface in which cells will be binned; default=(-20:20)*10
data	Halo data for one sample, loaded from *.rda file
statsByBand	logical; return stats broken down by interface bands (bins) as opposed to total stats; default=FALSE

Value

a list containing two tables: 'density' and 'area'

caitlinjones/halo documentation built on May 7, 2019, 8 a.m.