configureStudy: Configure study

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

Description

Set study parameters and write YAML file to be used as study config

Usage

configureStudy(study_name = NULL, study_dir = NULL,
  set_default_directory_struct = TRUE, config_dir = NULL,
  study_config_file = NULL, raw_data_dir = NULL, raw_data_files = NULL,
  data_dir = NULL, data_files = NULL, meta_dir = NULL,
  meta_files = NULL, annotations_dirs = NULL, annotations_files = NULL,
  drift_dir = NULL, drift_files = NULL, cohort_dir = NULL,
  infiltration_dir = NULL, fov_stats_dir = NULL,
  infiltration_density_dir = NULL, infiltration_density_file = NULL,
  infiltration_area_dir = NULL, infiltration_band_assignments_file = NULL,
  infiltration_area_file = NULL, fov_density_dir = NULL,
  fov_density_file = NULL, fov_area_dir = NULL, fov_area_file = NULL,
  plot_config_file = NULL, marker_analysis_config_file = NULL,
  cell_type_config_file = NULL, debug = TRUE,
  raw_marker_combo_table_file = NULL, pad = 20, drift_threshold = 0.1,
  updateExistingConfigFiles = TRUE, write_csv_files = TRUE, log = NULL,
  max_g = 5, band_width = 10, max_distance_from_interface = 360)

Arguments

study_name	name of study
study_dir	directory where all study output will be written
config_dir	directory where all configuration files are/will be
study_config_file	configuration file containing all study-wide parameters
raw_data_dir	location of RAW *.rda files (from Nick)
raw_data_files	list of RAW *.rda files (from Nick); may be specified instead of raw_data_dir
data_dir	location of exclusion-marked *.rda files to be used for analysis
data_files	list of exclusion-marked *.rda files to be used for analysis; may be used instead of specifying an entire directory
meta_dir	directory containing all meta data excel files
meta_files	list of meta data excel files; may be specified in addition to OR instead of entire meta_dir
annotations_dirs	root directory of ALL halo boundary annotations; currently set up to use subdir names to determine types of boundaries
drift_dir	directory containing *drift_summary.txt files to be used for marking exclusions
drift_files	list specifying certain *drift_summary.txt files to be used for marking exclusions; may be used instead of drift_dir
infiltration_dir	root directory for all infiltration analyses (within study dir)
fov_stats_dir	root directory for all total FOV-based analyses (within study dir)
infiltration_density_dir	directory for infiltration density analyses
infiltration_density_file	file containing (or to contain) infiltration density data
infiltration_area_dir	directory for infiltration area data
infiltration_area_file	file containing (or to contain) infiltration area data
fov_density_dir	directory for total FOV density analyses
fov_density_file	file containing (or to contain) total FOV density data
fov_area_dir	directory for total FOV area data
fov_area_file	file containing (or to contain) total FOV area data
plot_config_file	YAML file containing plot configuration, specifically matching cell types to colors
marker_analysis_config_file	YAML file detailing configuration of sets of markers to be analyzed
cell_type_config_file	YAML file in same format as marker_analysis_config_file, specifically for cell type markers
debug	logical indicating whether to print extra debug statements
raw_marker_combo_table_file	file containing (or to contain) counts of all possible marker combinations
pad	number in pixels to trim from images before analysis
drift_threshold	maximum percentage of drift allowed in order for a cell to be included in analyses
updateExistingConfigFiles	if providing existing configuration files, overwrite them with updated information as the pipeline progresses
write_csv_files	logical indicating whether to write intermediate data to CSV files
log	log file
max_g	????????
band_width	for infiltration analyses (area and density), band_width specifies the length of distance intervals from the tumor interface
set_default_directory_structure	logical indicating whether to set up default directory structure
annotations_file	*.rda file containing PARSED halo boundary annotations
maximum_distance_from_interface	maximum distance from tumor interface for a cell to be considered near the tumor boundary

Value

nothing

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