tpp2dImport: Import 2D-TPP data

Description Usage Arguments Value Examples

View source: R/tpp2dImport.R

Description

Imports data from 2D-TPP experiments by parsing a configTable and reading in corresponding data file or data frames containing raw data (sumionarea values) and creating a big data frame comprising all samples with respective fold changes

Usage

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tpp2dImport(
  configTable = NULL,
  data = NULL,
  idVar = "gene_name",
  addCol = NULL,
  intensityStr = "signal_sum_",
  qualColName = "qupm",
  nonZeroCols = "qssm",
  fcStr = NULL
)

Arguments

configTable

dataframe, or character object with the path to a file, that specifies important details of the 2D-TPP experiment. See Section details for instructions how to create this object.

data

single dataframe, containing raw measurements and if already available fold changes and additional annotation columns to be imported. Can be used instead of specifying the file path in the configTable argument.

idVar

character string indicating which data column provides the unique identifiers for each protein.

addCol

additional column names that specify columns in the input data that are to be attached to the data frame throughout the analysis

intensityStr

character string indicating which columns contain the actual sumionarea values. Those column names containing the suffix intensityStr will be regarded as containing sumionarea values.

qualColName

character string indicating which column can be used for additional quality criteria when deciding between different non-unique protein identifiers.

nonZeroCols

character string indicating a column that will be used for filtering out zero values.

fcStr

character string indicating which columns contain the actual fold change values. Those column names containing the suffix fcStr will be regarded as containing fold change values.

Value

A dataframe comprising all experimental data

Examples

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# 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")

TPP documentation built on Nov. 8, 2020, 5:55 p.m.