Import an abundance file — importExperiment • einprot

Import data from a quantification file (e.g. MaxQuant peptideGroups.txt, Proteome Discoverer Proteins.txt) into a SingleCellExperiment object. Typically sample-specific columns will be used to form assays, and other columns will be added as rowData columns.

importExperiment(
  inFile,
  iColPattern,
  includeOnlySamples = "",
  excludeSamples = "",
  ...
)

Arguments

inFile: Path to a tab-delimited input text file (e.g. MaxQuant peptideGroups.txt, Proteome Discoverer Proteins.txt or FragPipe combined_protein.tsv).
iColPattern: Character scalar defining a regular expression to identify sample columns. For MaxQuant output, this is typically one of "^iBAQ\.", "^LFQ\.intensity\." or "^Intensity\.". For Proteome Discoverer, it is typically "^Abundance\.", "^Abundance\.F[0-9]+\." or "^Abundance\.F.+\.Sample\.". For FragPipe, it is typically "\.MaxLFQ\.Intensity$". Columns matching the given pattern will form the first assay in the output object.
includeOnlySamples, excludeSamples: Character vectors defining regular expressions to match against the extracted columns to retain or exclude samples.
...: Additional arguments that will be passed on to QFeatures::readSummarizedExperiment (e.g., the number of rows to import).

Value

A list with two elements: a SingleCellExperiment object and a character scalar with the main assay name (this assay contains the values from the columns matching the provided iColPattern).

Author

Charlotte Soneson

Examples

sceL <- importExperiment(system.file("extdata", "mq_example",
                                     "1356_proteinGroups.txt",
                                     package = "einprot"),
                         iColPattern = "^iBAQ\\.")
sceL
#> $sce
#> class: SingleCellExperiment 
#> dim: 463 9 
#> metadata(1): colList
#> assays(9): iBAQ MS.MS.Count ... Peptides Identification.type
#> rownames(463): 1 2 ... 462 463
#> rowData names(35): Protein.IDs Majority.protein.IDs ...
#>   Oxidation.M.site.IDs Oxidation.M.site.positions
#> colnames(9): Adnp_IP04 Adnp_IP05 ... RBC_ctrl_IP02 RBC_ctrl_IP03
#> colData names(0):
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> 
#> $aName
#> [1] "iBAQ"
#>