readSCPfromDIANN.Rd
This function takes the output tables from DIA-NN and converts them into a QFeatures object using the scp framework.
readSCPfromDIANN(
colData,
reportData,
extractedData = NULL,
multiplexing = "none",
...
)
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).
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.
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
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()
An instance of class QFeatures. The expression data of each acquisition run is stored in a separate assay as a SingleCellExperiment object.