prepareData {mixlow}R Documentation

Prepares raw data for use by other functions

Description

Prepares data for use by doNls and other functions.

Usage

prepareData(trayData, drugs, trays, cellLines)

Arguments

trayData A list returned from readDataFile
drugs A vector of drug names used to subset data
trays A vector of tray names used to subset data
cellLines A vector of cell line names used to subset data

Details

Data contained in a trayData object (produced by use of the readDataFile function) must be adjusted before it can be used by other functions of this package. The prepareData function adjusts observed responses based on responses in the optical control (“blank”) wells. The method used to adjust observed responses is stated in the data file (methods are either “bbt” or “bbc”). For method “bbc”, a fourth order polynomial is fit to the concentration-dependent optical control data. Predictions for each concentration are subtracted from the observed experimental responses. For type “bbt”, the average optical control response is subtracted from all observed responses.

To aid in forming the arguments drugs, trays, and cellLines, vectors of each can be obtained using the convenience functions getDrugs, getTrays, and getCellLines.

Value

A list of class mixlowData with the following components:

concentrationResponse A data frame containing adjusted concentration-response data
drugRatios A data frame containing drug ratios
plottingData A list used by plotMixlowData in plotting

Author(s)

John Boik jcboik@stanford.edu

See Also

readDataFile, plotMixlowData, summarizeData

Examples

# trayData data object is obtained using the readDataFile function
data(trayData)
trays <- getTrays(trayData)
cellLines <- getCellLines(trayData)
mixlowData <- prepareData(trayData=trayData, drugs="drug1", trays=trays[1:9],
    cellLines=cellLines[1])

[Package mixlow version 0.01.1 Index]