tpp2dCreateReport {TPP} | R Documentation

## Create Report of 2D-TPP analysis

### Description

Creates a markdown pdf file that summarizes the 2D-TPP analysis by reporting e.g. R version and package versions used

### Usage

    tpp2dCreateReport(data = NULL, configFile = NULL, resultPath = NULL,
      documentType = "html_document", configTable = NULL,
      normalize = TRUE, methods = c(""), idVar = "gene_name",
      fcStr = "rel_fc_", fcStrUpdated = "norm_rel_fc_",
      intensityStr = "signal_sum_", addCol = NULL, fcTolerance = NA,
      r2Cutoff = NA, fcCutoff = NA, slopeBounds = c(NA, NA),
      fTest = FALSE, trRef = "none")

### Arguments

`data` | output data frame from an 2D-TPP analysis
`configFile` | character string containing a valid system path to a file which summarizes the experimental details of the 2D-TPP experiment or respective data frame
`resultPath` | character string containing a system path to where the report should be written
`documentType` | character string indicating which document type the report should have default: "html_document", alternatives: "pdf_document"
`configTable` | data frame summarizing the experimental details of the 2D-TPP experiment
`normalize` | boolean flag indicating whether median normalization has been performed
`methods` | vector of characters which indicate which methods have been used
`idVar` | unique protein identifier prefix
`fcStr` | fold change identifier prefix
`fcStrUpdated` | character string matching the fold change columns after normalization has been performed
`intensityStr` | intensity values prefix
`addCol` | vector of strings indicating which additional data columns were imported
`fcTolerance` | tolerance for the fcCutoff parameter
`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
`fTest` | boolean variable stating whether an fTest was performed
`trRef` | character string containing a valid system path to a previously generated TPP-TR reference object

### Value

A pdf or html report which summarizes all parameters that were set

[Package TPP version 3.15.3 Index]