tpptrAnalyzeMeltingCurves {TPP} | R Documentation |
Compute p-values for the pairwise comparisons of melting curve shifts between different conditions.
tpptrAnalyzeMeltingCurves( data, pValMethod = "robustZ", pValFilter = list(minR2 = 0.8, maxPlateau = 0.3), pValParams = list(binWidth = 300) )
data |
list of ExpressionSets containing fold changes and metadata. Their featureData fields contain the fitted melting curve parameters. |
pValMethod |
Method for p-value computation. Currently restricted to 'robustZ' (see Cox & Mann (2008)). |
pValFilter |
optional list of filtering criteria to be applied before p-value computation. |
pValParams |
optional list of parameters for p-value computation. |
The pValParams
argument is a list that can contain optional parameters
for the chosen p-value computation pValMethod
. The following options are
available:
pValMethod = "robustZ"
:
pValParams=list(binWidth=[your_binWidth])
.
A data frame in which the fit results are stored row-wise for each protein.
Cox, J., & Mann, M. (2008). MaxQuant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification. Nature biotechnology, 26(12), 1367-1372.
data(hdacTR_smallExample) tpptrData <- tpptrImport(hdacTR_config, hdacTR_data) tpptrNorm <- tpptrNormalize(data=tpptrData, normReqs=tpptrDefaultNormReqs()) normalizedData <- tpptrNorm$normData ## Not run: # Fit melting curves to each protein # (can take some time depending on device used): fittedData <- tpptrCurveFit(normalizedData, nCores=1) resultTable <- tpptrAnalyzeMeltingCurves(fittedData) subset(resultTable, fulfills_all_4_requirements)$Protein_ID ## End(Not run)