format_data: Format raw experimental data for subsequent processing

In Guilz/rfret: Analyze FRET Binding Data

Description

This function formats data for subsequent processing. It will accept all data files in a given directory, or any number of data files specified by their names, or any number of dataframes supplied as a named list, or even a single dataframe supplied as is.

Usage

format_data(input, data_type, skip_lines = 0, metadata_json = NULL)

Arguments

input	A directory name, a vector of file names, a single dataset already loaded in memory as a dataframe, or a list of datasets already loaded in memory as dataframes.
data_type	A character string describing which type of data is supplied for pre-processing. Currently supported options are "fret" and "fp".
skip_lines	The number of lines to skip at the beginning of CSV files (usually containing header information before the actual data starts).
metadata_json	A JSON file describing mappings between internal names and metadata information in the actual data files. It can contain the following entries, independent of the type of data: content The name of the column describing sample content. Default value: "Content". concentration The name of the column containing the concentration series. Default value: "concentration". titration The name describing points of the titration series. Default value: "titration". buffer_only The name describing points of the control series with only buffer. Default value: "buffer_only". A metadata file for FRET datasets can also contain the following entries: fret_channel The name of the column containing fluorescence intensities from the FRET channel. Default value: "fret_channel". acceptor_channel The name of the column containing fluorescence intensities from the acceptor channel. Default value: "acceptor_channel". donor_channel The name of the column containing fluorescence intensities from the donor channel. Default value: "donor_channel". acceptor_only The name describing points of the control series with only acceptor. Default value: "acceptor_only". donor_only The name describing points of the control series with only donor. Default value: "donor_only". A metadata file for FP/FA datasets can also contain the following entries: parallel The name of the column containing fluorescence intensities from the parallel channel. Default value: "parallel". perpendicular The name of the column containing fluorescence intensities from the perpendicular channel. Default value: "perpendicular". polarization The name of the column containing fluorescence polarization values, if already calculated by the instrument. Default value: "polarization". anisotropy The name of the column containing fluorescence anisotropy values, if already calculated by the instrument. Default value: "anisotropy". intensity The name of the column containing total fluorescence intensity values, if already calculated by the instrument. Default value: "intensity". baseline The name describing points of the baseline series (fluorescent probe only, without titrant molecule). Default value: "baseline".

Value

A single dataframe with the combined input data, containing 8 columns: Experiment, Type, Replicate, Observation, fret_channel, acceptor_channel, donor_channel and concentration. Rows with missing values will be dropped.

Guilz/rfret documentation built on Oct. 18, 2021, 2:14 p.m.