createPlateInput: Create a template for plate annotation file

In lujunyan1118/DrugScreenExplorer_dev: A pipeline for processing drug sensitivity screen data

Description

This function creates a tab-separated values (tsv) file required for annotating plates, for example, the sample ID or patient ID for each plate. Users can use the file created by this function as a starting point for preparing the plate annotation file required by the readScreen() function. Users can also prepare the plate annotation file from scratch, as long as it follows the format requirement. More information is available in the package vignette.

Usage

createPlateInput(rawDir, file, entries = c(), batchAsFolder = FALSE)

Arguments

rawDir	a character string specifying the directory of the raw data folder
file	the output file name and path for the plate annotation file
entries	a vector of character strings to use as the column names in the plate annotation file (optional)
batchAsFolder	a logical value, whether the raw data from different batches are stored in different sub-folders. The default value is FALSE. If TRUE, the folder names will be used as batch identifiers automatically.

Value

This function creates a tab-separated values (tsv) file in the working directory.

Examples

# create a template for plate annotation file
rawFolder <- system.file('testData/rawData', package = 'DrugScreenExplorer')
createPlateInput(rawDir = rawFolder, file = 'plateAnno.tsv',
    entries = c('sampleID', 'patientID'))
# see vignette for more instructions

lujunyan1118/DrugScreenExplorer_dev documentation built on Dec. 21, 2021, 12:42 p.m.