analyze2DTPP: Analyze a 2D-TPP experiment
In DoroChilds/TPP: Analyze thermal proteome profiling (TPP) experiments

Description Usage Arguments Details Value References Examples

Performs the whole analysis workflow for 2D-TPP experiment by invoking routines for data import, data processing, fold change computation, median normalization, TPP-CCR curve fitting, plotting and production of the result table.

analyze2DTPP(
  configTable,
  data = NULL,
  resultPath = NULL,
  idVar = "gene_name",
  fcStr = NULL,
  intensityStr = "signal_sum_",
  naStrs = c("NA", "n/d", "NaN", "<NA>"),
  methods = "doseResponse",
  qualColName = "qupm",
  compFc = TRUE,
  normalize = TRUE,
  addCol = NULL,
  nCores = 1,
  nonZeroCols = "qssm",
  fcTolerance = 0.1,
  r2Cutoff = 0.8,
  fcCutoff = 1.5,
  slopeBounds = c(1, 50),
  fractAbund = FALSE,
  xlsxExport = TRUE,
  plotAll = FALSE,
  plotAllR2 = FALSE,
  plotSingle = FALSE,
  trRef = NULL,
  refFcStr = "norm_rel_fc_",
  addInfo = FALSE,
  createReport = "none",
  paletteName = "Spectral",
  configFile
)

`configTable`	dataframe, or character object with the path to a file, that specifies important details of the 2D-TPP experiment. See Section `details` for instructions how to create this object.
`data`	single dataframe, containing fold change measurements and additional annotation columns to be imported. Can be used instead of specifying the file path in the `configTable` argument.
`resultPath`	location where to store dose-response curve plots and results table.
`idVar`	character string indicating which data column provides the unique identifiers for each protein.
`fcStr`	character string indicating which columns contain the actual fold change values. Those column names containing the prefix `fcStr` will be regarded as containing fold change values. Only relevant if `compFC = FALSE`.
`intensityStr`	character string indicating which columns contain the actual sumionarea values. Those column names containing the prefix `intensityStr` will be regarded as containing sumionarea values.
`naStrs`	character vector indicating missing values in the data table. When reading data from file, this value will be passed on to the argument `na.strings` in function `read.delim`.
`methods`	vector of character strings that indicate which methods should be used for the analysis (default: c("doseResponse"), alternative: c("splineFit") or c("doseResponse", "splineFit"))
`qualColName`	character string indicating which column can be used for additional quality criteria when deciding between different non-unique protein identifiers.
`compFc`	boolean flag which indicates whether to perform fold change computation regarding reference column from sumionareas (default: TRUE)
`normalize`	perform median normalization (default: TRUE).
`addCol`	character vector indicating which additional columns to include from the input data
`nCores`	either a numerical value given the desired number of CPUs, or 'max' to automatically assign the maximum possible number (default).
`nonZeroCols`	character string indicating a column that will be used for filtering out zero values.
`fcTolerance`	tolerance for the fcCutoff parameter. See details.
`r2Cutoff`	Quality criterion on dose response curve fit.
`fcCutoff`	Cutoff for highest compound concentration fold change.
`slopeBounds`	Bounds on the slope parameter for dose response curve fitting.
`fractAbund`	boolean variable, if set to TRUE additional information concerning sumionarea fractional abundance and dmso1 vs. dmso2 of adjacent temperatures is added to the output table
`xlsxExport`	produce results table in xlsx format and store at the location specified by the `resultPath` argument.
`plotAll`	boolean value indicating whether all dose response curves should be generated. Deactivating plotting decreases runtime.
`plotAllR2`	boolean value indicating whether all dose response curves which fulfill the demanded criteria (Rsquared, maximum plateau) should be generated. Deactivating plotting decreases runtime.
`plotSingle`	boolean value indicating whether all dose response curves which fulfill the demanded criteria (Rsquared, maximum plateau) should be generated. Deactivating plotting decreases runtime.
`trRef`	character string containing a valid system path to a previously generated TPP-TR reference object
`refFcStr`	character string indicating which columns in the reference data set contain the fold change values
`addInfo`	boolean variable, if set to TRUE additional information on counts of stabilization and destabilization of each protein is added to the output table
`createReport`	character string indicating whether a markdown report should be created and which format it have (default: "html_document", alternative: "pdf_document" or "none")
`paletteName`	color palette (see details).
`configFile`	DEPRECATED

Invokes the following steps:

Import data using the tpp2dImport function.
Remove zero sumionarea values.
Compute fold changes from raw data (sumionarea)
Perform normalization by fold change medians (optional) using the tpp2dNormalize function. To perform normalization, set argument normalize=TRUE.

paletteName specifies the color palette to be used by the brewer.pal function from the RColorBrewer package to assign a separate color to each concentration.

A data frame in which the model results (slopes and pEC50 values) are stored row-wise for each protein and administered temperatures.

Becher, I., Werner, T., Doce, C., Zaal, E. A., Berkers, C. R., T"ogel, I., Salzer, E., Bantscheff, M., Savitski, M. M. (2016) Thermal profiling reveals phenylalanine hydroxylase as an off-target of panobinostat. Nature Chemical Biology, 12(11), 908-910.

data(panobinostat_2DTPP_smallExample)
config_tpp2d <- panobinostat_2DTPP_config
data_tpp2d <- panobinostat_2DTPP_data
tpp2dResults <- analyze2DTPP(configTable = config_tpp2d, 
                             data = data_tpp2d,
                             methods=c("doseResponse"),
                             createReport="none",
                             nCores=1,
                             idVar = "representative",
                             addCol = "clustername",
                             intensityStr = "sumionarea_protein_",
                             nonZeroCols = "qusm")