normalizePlate: Per-plate normalization

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

Description

This function calculates the percent inhibition or normalized viability values for each plate based on the control wells on the same plate.

Usage

normalizePlate(
  screenData,
  method = "negatives",
  discardLayer = 0,
  bySample = FALSE
)

Arguments

screenData	a data frame that contains the output from the readScreen() function.
method	a character string, either 'negatives' or 'both', specifying the method of per-plate normalization. If 'negatives' is used, the raw signals on the plate will be divided by the median signal intensity of negative control wells on the same plate. If 'both' is used, a 'normalized percent inhibition (NPI)' is applied in a per-plate basis. NPI measures the extent to which the signal of interest is diminished compared to a positive control: NPI = (Neg - x)/(Neg - Pos). The default value is 'negatives'.
discardLayer	an integer value. To avoid the impact of incubation effect on the negative controls, a certain number of the exterior layers on the plate can be ignored when calculating the median of control wells. 0 means do not discard any control wells.
bySample	a logical value, indicates whether normalized the viability by sample rather than by plate. This is for the situation that multiple samples are on the same plate.

Value

This function will add one column, normVal, which is the normalized viability based on user-specified normalization method, to the input data frame.

Examples

rawFolder <- system.file('testData/rawData', package = 'DrugScreenExplorer')
plateFile <- system.file('testData/plateAnno/plateAnno.tsv', package = 'DrugScreenExplorer')
wellFile <- system.file('testData/wellAnno/wellAnno.tsv', package = 'DrugScreenExplorer')
# Read in screen data without normalization
screenData <- readScreen(rawDir = rawFolder, plateAnnotationFile = plateFile,
    wellAnnotationFile = wellFile,
    rowRange = c(3,18), colRange = 2,
    sep = '[;\t]',
    negWell <- c('DMSO','PBS'), posWell = c(),
    normalization = FALSE)

# Perform a normalization step separately
screenData <- normalizePlate(screenData, method = 'negatives', discardLayer = 2)

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