calculateFOVStats: Calculate total area and density of entire FOVs

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

Description

Calculate total area and density of FOVs that do not contain tumors

Usage

calculateFOVStats(aFiles, data, markerSet, cellTypeName, maxG,
  writeCSVfiles = TRUE, funcMarker = NULL, sortByMarker = NULL,
  skipTumorSamples = TRUE, outDir)

Arguments

aFiles	a vector of Halo boundary annotation files, with '.annotations' extension in XML format
data	Halo data for one sample loaded from a *.rda
markerSet	a vector markers to calculate density for
cellTypeName	a name to represent the cell types in marker file
maxG	the maximum factor of 10 to use for generating random points for area calculation
writeCSVfiles	logical indicating whether to write density and area tables to file;
funcMarker	this marker will be added to all markers in markerSet in order to compare cells that are +/- for this functional marker [ TO DO: REWORD THIS ]
outDir	if writeCSVfiles=T, directory to which these files will be written

Value

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

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