tpp2dCreateTPPTRreference {TPP} | R Documentation

## Create TPP-TR reference for 2D-TPP experiment

### Description

Performs a reference analysis of a TPP-TR experiment and generates boxplots for the distribution of fold changes at the different temperatures if desired.

### Usage

    tpp2dCreateTPPTRreference(
      trConfigTable = NULL,
      trDat = NULL,
      resultPath = NULL,
      outputName = NULL,
      createFCboxplots = FALSE,
      idVar = "gene_name",
      fcStr = "rel_fc_",
      qualColName = "qupm",
      normalize = TRUE
    )

### Arguments

`trConfigTable` | config file for a reference TR dataset
`trDat` | list of dataframes, 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` | character string containing a valid system path to which folder output files will be written
`outputName` | character string which will be used as name of the output folder
`createFCboxplots` | boolean flag indicating whether quality control boxplots are to be plotted
`idVar` | character string indicating which column of the data table contains the unique protein ids
`fcStr` | character string indicating which columns contain fold changes
`qualColName` | character string indicating which column contain protein identification quality measures
`normalize` | boolean argument stating whether the data should be normalized or not

### Value

A TPP-TR reference object for a certain cell line with different supporting files in a desired output directory. The main object which is of interest for further analysis is the `trRefData.RData` file. This is the file to which a referencing system path has to be indicated when a function as `tpp2dSplineFitAndTest` require to input a TPP-TR reference object. The RData file consists of list carrying four different items:

1. tppCfgTable: the TPP-TR configtable which was used for generating this object

2. sumResTable a list of two elements 1. detail: the exact result data from the TR analysis and 2. summary. a summary of the analyzed TR data comprising the median and standard deviation values of the measurements at the different temperatures (encoded by the isobaric labels)

3. temperatures a table listing the temperatures which were used in the TR experiment in the different replicates

4. lblsByTemp a table matching each temperature to an isobaric label

[Package TPP version 3.16.5 Index]