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

Description Usage Arguments Value

View source: R/tpp2dCreateTPPTRreference.R


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


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



config file for a reference TR dataset


character string containing a valid system path to which folder output files will be written


character string which will be used as name of the output folder


boolean flag indicating whether quality control boxplots are to be plotted


character string indicating which column of the data table contains the unique protein ids


character string indicating which columns contain fold changes


character string indicating which column contain protein identification quality measures


boolean argument stating whether the data should be normalized or not


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

Bioconductor-mirror/TPP documentation built on July 7, 2017, 11:01 p.m.