tpp2dNormalize: Median normalization of protein fold changes of 2D-TPP data

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

Description

Normalizes fold changes retrieved from 2D-TPP experiment by dividing by the median fold change

Usage

tpp2dNormalize(configTable = NULL, data, fcStr = NULL)

Arguments

configTable	DEPRECATED
data	data frame that contains the data for the 2D-TPP experiment
fcStr	DEPRECATED

Value

A dataframe identical to the input dataframe except that the columns containing the fold change values have been normalized by their median.

Examples

# Preparation:
data(panobinostat_2DTPP_smallExample)

# Import data:
datIn <- tpp2dImport(configTable = panobinostat_2DTPP_config,
                      data = panobinostat_2DTPP_data,
                      idVar = "representative",
                      addCol = "clustername",
                      intensityStr = "sumionarea_protein_",
                      nonZeroCols = "qusm")

# Compute fold changes:
datFC <- tpp2dComputeFoldChanges(data = datIn)

# Perform median normalization:
datNorm <- tpp2dNormalize(data = datFC)

# View updated attributes. Now contain field 'fcStrNorm' indicating prefix
# of the fold change columns after normalization.
attr(datNorm, "importSettings")["fcStrNorm"]
  

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