prepareData {mixlow} | R Documentation |
Prepares data for use by doNls
and other functions.
prepareData(trayData, drugs, trays, cellLines)
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 |
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
.
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 |
John Boik jcboik@stanford.edu
readDataFile
, plotMixlowData
,
summarizeData
# 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])