Import sage identification results

This function imports sage identification results as a PSMatch::PSM() object.

sagePSM(
  idTable,
  spectrum = "scannr",
  peptide = "peptide",
  protein = "proteins",
  decoy = "label",
  rank = "rank",
  score = "sage_discriminant_score",
  fdr = "spectrum_q",
  ...
)

Arguments

idTable: character(1) containing the path to the identification results, typically "results.sage.tsv", or a data.frame containing the identification results.
spectrum: character(1) variable name that defines a spectrum in the PSM data. Default are "scannr".
peptide: character(1) variable name that defines a peptide in the PSM data. Detaults are "peptide".
protein: protein character(1) variable name that defines a protein in the PSM data. Detaults are "proteins".
decoy: character(1) variable name that defines a decoy hit in the PSM data. Detaults are "label".
rank: character(1) variable name that defines the rank of the peptide spectrum match in the PSM data. Default is "rank".
score: character(1) variable name that defines the PSM score. default is "sage_discriminant_score".
fdr: character(1) variable name that defines the spectrum FDR (or any relevant reliability score that can be used for filtering, such as the PEP) in the PSM data. Default is "spectrum_q".
...: Additional arguments passed to read.delim().

Value

An instance of class PSM().

Author

Laurent Gatto

Examples


## Add the data to the package's cache if they
## aren't already available

if (!sagerAvailableData("id"))
  sagerAddData("id")
basename(f <- sagerIdData())
#> [1] "92fe02655fa2c_results.sage.tsv"

sagePSM(f)
#> PSM with 977 rows and 34 columns.
#> names(34): peptide proteins ... protein_fdr ms1_intensity