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

Description Usage Arguments Value

View source: R/tpp2dCreateTPPTRreference.R

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

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tpp2dCreateTPPTRreference(trConfigTable = 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

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


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