tpp2dCreateTPPTRreference: Create TPP-TR reference for 2D-TPP experiment

In DoroChilds/TPP: Analyze thermal proteome profiling (TPP) experiments

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

DoroChilds/TPP documentation built on Oct. 31, 2021, 4:38 a.m.