fetchPeptidesInfo: Get scores of all peptides

Description Usage Arguments Value Author(s) See Also Examples

Description

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

Usage

1
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, shubh.gupta@mail.utoronto.ca

ORCID: 0000-0003-3500-8152

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

See Also

getPeptideQuery, getPeptideScores

Examples

1
2
3
4
5
6
7
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.