Import data from Spectronaut into a SingleCellExperiment object

Import data from a Spectronaut quantification file into a SingleCellExperiment object. Note that Spectronaut support in einprot is currently experimental - please be aware that the interface may change, and interpret results with caution.

importSpectronaut(
  inFile,
  fileType = "pg_pivot",
  outLevel = "pg",
  iColPattern = ".PG.Quantity$",
  includeOnlySamples = "",
  excludeSamples = "",
  stopIfEmpty = FALSE,
  aName = "PG.Quantity",
  ...
)

Arguments

inFile

Path to a tab-delimited input text file from Spectronaut.

fileType

Character scalar indicating the type of input file; either "pg_pivot" or "long_format".

outLevel

Character scalar indicating the desired output level; currently only "pg" (protein group) is supported.

iColPattern

Character scalar defining a regular expression to identify sample columns (only used if fileType is "pg_pivot". This is typically one of ".PG.Quantity$" or ".PG.IBAQ$". 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.

stopIfEmpty

Logical scalar, whether to raise an error if no columns matching the patterns are found.

aName

Character scalar giving the column from which to get the values for the main assay. Only used if fileType is "long_format".

...

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.

Author

Charlotte Soneson