Read DIA-NN output as a QFeatures objects for single-cell proteomics data

Use the readSCPfromDIANN() function from the scp package to lead DIA-NN report files. This function is kept for the vignette backward compatibility.

readSCPfromDIANN(
  colData,
  reportData,
  extractedData = NULL,
  multiplexing = "none",
  ...
)

Arguments

colData: A data.frame or any object that can be coerced to a data.frame. colData is expected to contains all the sample annotations. We require the table to contain a column called File.Name that links to the File.Name in the DIA-NN report table. If multiplexing = "mTRAQ", we require a second column called Label that links the label to the sample (the labels identified by DIA-NN can be retrieved from Modified Sequence column in the report table).
reportData: A data.frame or any object that can be coerced to a data.frame that contains the data from the Report.tsv file generated by DIA-NN.
extractedData: A data.frame or any object that can be coerced to a data.frame that contains the data from the *_ms1_extracted.tsv file generated by DIA-NN. This argument is optional and is only applicable for mulitplixed experiments
multiplexing: A character(1) indicating the type of multiplexing used in the experiment. Provide "none" if the experiment is label-free (default). Available options are: "mTRAQ".
...: Further arguments passed to readSCP()

Value

An instance of class QFeatures. The expression data of each acquisition run is stored in a separate assay as a SingleCellExperiment object.