tppccrImport: Import TPP-CCR dataset for analysis by the `TPP` package.

Description

tppccrImport imports a table of protein fold changes and stores them in an ExpressionSet for use in the TPP package.

Usage

tppccrImport(configTable, data = NULL, idVar = "gene_name", fcStr = "rel_fc_", naStrs = c("NA", "n/d", "NaN", ""), qualColName = "qupm", nonZeroCols = "qssm")

Arguments

configTable

either a dataframe or the path to a spreadsheet. In both cases it specifies necessary information of the TPP-CCR experiment.

data

dataframe containing fold change measurements and additional annotation columns to be imported. Can be used instead of specifying the file path in configTable.

idVar

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

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.

naStrs

character vector indicating missing values in the data table. When reading data from file, this value will be passed on to the argument na.strings in function read.delim.

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.

Value

ExpressionSet object storing the measured fold changes, as well as row and column metadata. In each ExpressionSet S, the fold changes can be accessed by exprs(S). Protein expNames can be accessed by featureNames(S). Isobaric labels and the corresponding concentrations are returned by S$label and S$concentration.

Details

The imported dataset has to contain measurements obtained by a TPP-CCR experiment. Fold changes need to be pre-computed using the lowest concentration as reference. The dataset can be specified by filename in the configTable argument, or given directly in the data argument The default settings are adjusted to analyse data of the pyhton package isobarQuant. You can also customise them for your own dataset. The configTable argument is a dataframe, or the path to a spreadsheet (tab-delimited text-file without quoted strings, or xlsx format). Information about each experiment is stored row-wise. It contains the following columns:

Path: location of the datafile. Alternatively, data can be directly handed over by the data argument.
Experiment: unique experiment name.
Label columns: each isobaric label names a column that contains the concentration administered for the label in the individual experiments.

During data import, proteins with NAs in the data column specified by idVar receive unique generic IDs so that they can be processed by the package.

Examples

Run this code

data(hdacCCR_smallExample)
tppccrData <- tppccrImport(configTable=hdacCCR_config, 
data = hdacCCR_data)