wrapperCalibrationPlot: Performs a calibration plot on an 'MSnSet' object, calling...
In samWieczorek/DAPAR: Tools for the Differential Analysis of Proteins Abundance with R
wrapperCalibrationPlot R Documentation
Performs a calibration plot on an MSnSet object,
calling the cp4p package functions.
Description
This function is a wrapper to the calibration.plot method of the
cp4p package for use with MSnSet objects.
Usage
wrapperCalibrationPlot(vPVal, pi0Method = "pounds")
Arguments
vPVal
A dataframe that contains quantitative data.
pi0Method
A vector of the conditions (one condition per sample).
Value
A plot
Author(s)
Samuel Wieczorek
Examples
utils::data(Exp1_R25_prot, package='DAPARdata')
obj <- Exp1_R25_prot[1:1000]
level <- obj@experimentData@other$typeOfData
metacell.mask <- match.metacell(GetMetacell(obj), 'missing', level)
indices <- GetIndices_WholeMatrix(metacell.mask, op='>=', th=1)
obj <- MetaCellFiltering(obj, indices, cmd='delete')
qData <- Biobase::exprs(obj$new)
sTab <- Biobase::pData(obj$new)
limma <- limmaCompleteTest(qData,sTab)
wrapperCalibrationPlot(limma$P_Value[,1])
samWieczorek/DAPAR documentation built on May 6, 2022, 5:30 p.m.
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| wrapperCalibrationPlot | R Documentation |
Performs a calibration plot on an MSnSet object,
calling the cp4p package functions.
Description
This function is a wrapper to the calibration.plot method of the
cp4p package for use with MSnSet objects.
Usage
wrapperCalibrationPlot(vPVal, pi0Method = "pounds")
Arguments
vPVal |
A dataframe that contains quantitative data. |
pi0Method |
A vector of the conditions (one condition per sample). |
Value
A plot
Author(s)
Samuel Wieczorek
Examples
utils::data(Exp1_R25_prot, package='DAPARdata') obj <- Exp1_R25_prot[1:1000] level <- obj@experimentData@other$typeOfData metacell.mask <- match.metacell(GetMetacell(obj), 'missing', level) indices <- GetIndices_WholeMatrix(metacell.mask, op='>=', th=1) obj <- MetaCellFiltering(obj, indices, cmd='delete') qData <- Biobase::exprs(obj$new) sTab <- Biobase::pData(obj$new) limma <- limmaCompleteTest(qData,sTab) wrapperCalibrationPlot(limma$P_Value[,1])
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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