tpp2dComputeFoldChanges: Compute 2D-TPP fold changes

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

Description

Computes fold changes by calculating fold changes of the sumionarea relative to the reference column.

Usage

tpp2dComputeFoldChanges(
  configTable = NULL,
  data,
  intensityStr = NULL,
  fcStr = NULL,
  newFcStr = "rel_fc_"
)

Arguments

configTable	DEPRECATED
data	dataframe that contain the data for the 2D-TPP experiment
intensityStr	DEPRECATED
fcStr	DEPRECATED
newFcStr	character string indicating how columns that will contain the actual fold change values will be called. The suffix newFcStr will be pasted in front of the names of the experiments.

Value

A data.frame with additional columns with constitute fold changes calculated with respect to the intensity values of the zero treatment column

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")

# View attributes of imported data (experiment infos and import arguments):
attr(datIn, "importSettings") %>% unlist
attr(datIn, "configTable")

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

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

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