tppccrCurveFit {TPP} | R Documentation |
tppccrCurveFit
fits logistic dose response curves to fold
change measurements of a TPP-CCR experiment.
tppccrCurveFit(data = NULL, fcTable = NULL, cpdEffects = NULL, slopeBounds = c(1, 50), nCores = "max", verbose = FALSE)
data |
list of expressionSet objects containing protein fold changes for dose response curve fitting. |
fcTable |
optional long table with fold changes for each experiment.
Can be provided instead of the input argument |
cpdEffects |
optional long table of compound effects per protein and
experiment. Can be provided instead of the input argument |
slopeBounds |
bounds on the slope parameter for dose response curve fitting. |
nCores |
either a numerical value given the desired number of CPUs, or 'max' to automatically assign the maximum possible number (default). |
verbose |
print name of each fitted protein to the command line as a means of progress report. |
data
is a list of expressionSet objects created by
tppccrImport
. If desired, it can be already preprocessed by
tppccrNormalize
or tppccrTransform
. It contains
the isobaric labels and administered drug concentrations in the
phenoData
and user-defined protein properties in the
featureData
. Protein IDs are stored in the featureNames
.
Measurements and compound effects for curve fitting can be provided
by the arguments fcTable
and cpdEffects
, instead of being
stored in expressionSets in data
.
If specified, fcTable
needs to be a long
table with column names "id" (the protein names), "concentration" (the fold
changes), "labelName" (the isobaric label to each measurement), and
"experiment" (e.g. "Vehicle_1" or "Panobinostat_1").
If specified, cpdEffects
needs to be a long
table with column names "id" (the protein names), "cpdEff" (character
vector of compound effects, may contain NAs), and
"experiment" (e.g. "Vehicle_1" or "Panobinostat_1").
A list of expressionSet objects storing fold changes, the fitted
curve parameters, as well as row and column metadata. In each expressionSet
S
, the fold changes can be accessed by Biobase::exprs(S)
. Protein
expNames can be accessed by featureNames(S)
. Isobaric labels and the
corresponding concentrations are returned by S$label
and
S$concentration
. The fitted curve parameters are stored in
codefeatureData(S).
tppccrImport
, tppccrNormalize
,
tppccrTransform
data(hdacCCR_smallExample) tppccrData <- tppccrImport(configTable=hdacCCR_config, data=hdacCCR_data) tppccrNorm <- tppccrNormalize(data=tppccrData) tppccrTransformed <- tppccrTransform(data=tppccrNorm) tppccrFitted <- tppccrCurveFit(data=tppccrTransformed, nCores=1)