flattenMetaData: Flatten meta data for a single study

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

Description

Given all available meta data files for a single study, flatten all data into three tables: (1) SlideAnnotation - all information regarding samples and FOV (2) MarkerAnnotation - all information describing individual markers (3) MarkerCombinationAnnotation - all information describing important marker combinations

Usage

flattenMetaData(metaDir = NULL, metaFiles = NULL, sampAnnFile = NULL,
  fovAnnFile = NULL, cellTypesFile = NULL, haloPanelsFile = NULL,
  markerDescFile = NULL)

Arguments

metaDir	directory containing all available meta data files in XLSX format; default=NULL
metaFiles	vector of meta data files; an alternative to providing metaDir; default=NULL
sampAnnFile	sample annotation file in XLSX format; if given, this value will override a sample annotation file found in metaDir or metaFiles; default=NULL
fovAnnFile	FOV annotation file in XLSX format; if given, this value will override a FOV annotation file found in metaDir or metaFiles; default=NULL
cellTypesFile	XLSX file describing all known cell types (marker combinations); if given, this value will override a cell types file found in metaDir or metaFiles; default=NULL
haloPanelsFile	XLSX file describing all halo panels; if given, this value will override a halo panels file found in metaDir or metaFiles; default=NULL
markerDescFile	XLSX file describing individual markers; if given, this value will override a marker description file found in metaDir or metaFiles; default=NULL
unreasonalbesFile	#### MOST LIKELY WILL BE REMOVED

Value

a list containing three data frames: SlideAnnotation, MarkerAnnotation and MarkerCombinationAnnotation

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