import2dDataset {TPP2D} | R Documentation |
Import 2D-TPP dataset using a config table
import2dDataset(configTable, data, idVar = "representative", intensityStr = "sumionarea_protein_", fcStr = "rel_fc_protein_", nonZeroCols = "qssm", geneNameVar = "clustername", addCol = NULL, qualColName = "qupm", naStrs = c("NA", "n/d", "NaN"), concFactor = 1e+06, medianNormalizeFC = TRUE, filterContaminants = TRUE)
configTable |
character string of a file path to a config table |
data |
possible list of datasets from different MS runs corresponding to a 2D-TPP dataset, circumvents loading datasets referencend in config table, default is NULL |
idVar |
character string indicating which data column provides the unique identifiers for each protein. |
intensityStr |
character string indicating which columns contain raw intensities measurements |
fcStr |
character string indicating which columns contain the actual
fold change values. Those column names containing the suffix |
nonZeroCols |
column like default qssm that should be imported and requested to be non-zero in analyzed data |
geneNameVar |
character string of the column name that describes the gene name of a given protein in the raw data files |
addCol |
character string indicating additional column to import |
qualColName |
character string indicating which column can be used for additional quality criteria when deciding between different non-unique protein identifiers. |
naStrs |
character vector indicating missing values in the data table.
When reading data from file, this value will be passed on to the argument
|
concFactor |
numeric value that indicates how concentrations need to be adjusted to yield total unit e.g. default mmol - 1e6 |
medianNormalizeFC |
perform median normalization (default: TRUE). |
filterContaminants |
boolean variable indicating whether data should be filtered to exclude contaminants (default: TRUE). |
tidy data frame representing a 2D-TPP dataset
data("config_tab") data("raw_dat_list") import_df <- import2dDataset(configTable = config_tab, data = raw_dat_list, idVar = "protein_id", intensityStr = "signal_sum_", fcStr = "rel_fc_", nonZeroCols = "qusm", geneNameVar = "gene_name", addCol = NULL, qualColName = "qupm", naStrs = c("NA", "n/d", "NaN"), concFactor = 1e6, medianNormalizeFC = TRUE, filterContaminants = TRUE)