import_cell_profiler_data: Import CellProfiler data

In benvallin/banban: Analyse biological data

Import CellProfiler data

Description

import_cell_profiler_data() imports and tidy data generated by CellProfiler software.

Usage

import_cell_profiler_data(
  RelateObjects.data.files.list,
  IdentifyPrimaryObjects.data.files.list,
  prefix,
  main.object.nm = "neuron",
  main.object.structure.nm = "cell_body",
  metadata = FALSE
)

Arguments

RelateObjects.data.files.list	a string specifying the name of the .txt file which lists the names of all RelateObjects data files to be analysed. In the .txt list file, the RelateObjects file names must match the regex "RelateObjects_.*.csv" and be separated by a new line.
IdentifyPrimaryObjects.data.files.list	a string specifying the name of the .txt file which lists the names of all IdentifyPrimaryObjects data files to be analysed. In the .txt list file, the IdentifyPrimaryObjects file names must match the regex "IdentifyPrimaryObjects_.*.csv" and be separated by a new line.
prefix	a string specifying the path to the directory containing the .txt list files & .csv data files.
main.object.nm	a string indicating the name to be given to the main object defined by the main IdentifyPrimaryObjects module. The main object is the one (e.g.: neuron) within which other objects (e.g.: pSyn structures) are defined by additional IdentifyPrimaryObjects modules. Default is "neuron".
main.object.structure.nm	a string indicating the name which was used as part of the CellProfiler pipeline to define the main object in the main IdentifyPrimaryObjects module. Default is "cell_body".
metadata	a logical indicating if scaling-related metadata should be imported together with the CellProfiler data. If TRUE, the metadata should be provided as .xml files stored in a directory named "metadata" and located in the same directory as the .txt list files & .csv data files. Default is FALSE.

Details

Important note: the function requires all input files to be located in the same parent directory. Input files include .txt list files, .csv data files and metadata directory containing .xml metadata files.

Value

a tibble containing the tidied CellProfiler data (and possibly the associated metadata). Each row corresponds to a main object, columns store information related to accessory objects identified within the main object.

benvallin/banban documentation built on Sept. 29, 2023, 5:46 a.m.