get_experimental_log_file: get_experimental_log_file

In meaRtools: Micro-Electro Array (MEA) Analysis

Description

Extract data from experimental log file: a csv file with columns for well, treatment, dose, size and units.

Usage

get_experimental_log_file(file, master_chem_file = master_chem_file)

Arguments

file

spike-list csv file, one of the possible plate recording file formats available from Axion. Format: one spike and corresponding electrode name per row. See Axion biosystems website for details.

master_chem_file

A csv file containing the following columns: "Project", "Experiment.Date", "Plate.SN", "DIV", "Well", "Treatment", "Size", "Dose", and "Units". Empty wells must still be represented in file. If column is irrelavent to a given data set, then 'NA' or blank is sufficient. "Project" columm must match the first character string preceeding "_" in spike-list file name. e.g. exampleRecording_1012016_plate1_DIV1_spike_list.csv". Similarly, "Experiment.Data" and "Plate.SN" must match second and third character strings as separated by "_" in spike-list file name. "DIV" column does not need to be matched.

Value

list containing character vector of experimental log information.

well	well name e.g. "A4""
treatment	treatment on well e.g. 'WT'
size	size information of chemical treatment
dose	dose information for treatment
units	units of dosage e.g. uL/g

References

See http://www.axionbiosystems.com/products/software/ for details on spike-list csv file format

Examples

temp_path=tempdir()
master_chem_file<-paste0( temp_path,"/data",
   "/exampleRecording_1012016_plate1_expLog.csv" )
      
spike_list_file<-paste0( temp_path,"/data",
"/exampleRecording_1012016_plate1_DIV1_spike_list.csv" )

plate.data<-getxperimental.log.file( file=spike.list.file, master_chem_file = master_chem_file )

meaRtools documentation built on May 1, 2019, 7:32 p.m.