prepare_data: Prepare all input data for the revised probeset assignment

In friederhadlich/rePROBE: Revised probe assignment and updated probe-set annotation in microarrays

Description

The function wraps functions that can also be directly used in given order: prepare_input_arguments, create_project, prepare_chip, add_local_db, add_remote_db, add_dna, index_db, map_db, define_db_usage

Usage

prepare_data(
  WORK_PATH,
  PROJ_NAME,
  CHIP_PATH,
  SPECIES,
  NCPU,
  STRICT_MAPPING = T,
  ASK_QUESTIONS = T
)

Arguments

WORK_PATH	Working directory
PROJ_NAME	Project name
CHIP_PATH	Chip path with one pgf and one mps file
SPECIES	Species name in latin language, i.e. "Sus_scrofa"
NCPU	Number of threads to use
STRICT_MAPPING	Avoid SNP correction of probes
ASK_QUESTIONS	Answer questions automatically with their defaults

friederhadlich/rePROBE documentation built on Dec. 7, 2019, 12:26 a.m.