fetchPeptidesInfo: Get scores of all peptides

In Roestlab/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Description

Return a scores, pvalues, and qvalues for all peptides from the osw file.

Usage

fetchPeptidesInfo(oswName, runType, context)

Arguments

oswName	(char) path to the osw file.
runType	(char) This must be one of the strings "DIA_Proteomics", "DIA_Metabolomics".
context	(string) Context used in pyprophet peptide. Must be either "run-specific", "experiment-wide", or "global".

Value

(dataframe) with following columns:

peptide_id	(integer) a unique id for each precursor.
run	(character) as in SCORE_PEPTIDE.RUN_ID of osw files.
score	(numeric) as in SCORE_PEPTIDE.SCORE of osw files.
pvalue	(numeric) as in SCORE_PEPTIDE.PVALUE of osw files.
qvalue	(numeric) as in SCORE_PEPTIDE.QVALUE of osw files.

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2020) + GPL-3 Date: 2020-07-01

See Also

getPeptideQuery, getPeptideScores

Examples

dataPath <- system.file("extdata", package = "DIAlignR")
fileInfo <- getRunNames(dataPath = dataPath)
oswName <- fileInfo[["featureFile"]][1]
## Not run: 
precursorsInfo <- fetchPeptidesInfo(fileInfo, runType = "DIA_Proteomics", context = "experiment-wide")

## End(Not run)

Roestlab/DIAlignR documentation built on March 3, 2021, 9:09 a.m.