tpp2dImport {TPP} | R Documentation |
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
tpp2dImport(configTable = NULL, data = NULL, idVar = "gene_name", addCol = NULL, intensityStr = "signal_sum_", qualColName = "qupm", nonZeroCols = "qssm", fcStr = NULL)
configTable |
dataframe, or character object with the path to a file,
that specifies important details of the 2D-TPP experiment. See Section
|
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 |
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 |
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 |
A dataframe comprising all experimental data
# 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")