getTemplateCellTypeConfig: Generate a template marker configuration based on meta data

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

Description

Given either a table of cell types or a cell types file to be parsed, generate in list format a configuration of marker combinations to be used for downstream analysis. The purpose of this template is to provide the beginnings of any and all more complex configuration needed to calculate statistics and create plots of halo data

Usage

getTemplateCellTypeConfig(allCellTypes = NULL, cellTypesFile = NULL,
  writeYAML = TRUE, outDir = getwd())

Arguments

allCellTypes	flattened table containing all cell type file found in meta data files; if NULL, user must provide cellTypesFile to be parsed; default=NULL
cellTypesFile	cell types file in XLSX format structured according to meta data documentation rules; if NULL, user must provide a pre-generated table consisting of the data found in meta data file
writeYAML	logical indicating whether to write configuration to file; default=TRUE
outDir	directory where YAML file should be written; default=getwd()

Value

all marker information and default marker configuration values

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