cellDive.calculateInfiltrationDensity: Calculate infiltration density

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

Description

Generate table with five columns: Sample,SPOT,Band,Counts,Density

Usage

cellDive.calculateInfiltrationDensity(markerConfig, infiltrationAreas,
  bandAssignments, sampAnn, pp, updatedInfiltrationAreas,
  infiltrationDensityPrefix = "")

Arguments

markerConfig	parsed marker configuration (as returned by getMarkerConfig())
infiltrationAreas	area table containing Sample,SPOT,Band,Area
bandAssignments	table containing Band column where each value is an assignment for a single cell to a specific distance band around a tumor interface
sampAnn	table of all sample annotations
pp	list of all project parameters
updatedInfiltrationAreas	logical indicating whether infiltration areas were updated during the current pipeline run
infiltrationDensityPrefix	prefix added to infiltration_density_file/dir in list of project params; leave equal to "" to indicate no prefix added

Value

list of three items: (1) dat = table including Sample,SPOT,Band,Counts,Density (2) updated = logical indicating whether table being returned was generated (TRUE) or loaded from existing file (FALSE) (3) pp = updated list of project parameters

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