getPeptideScores: Get scores of peptide

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

Description

Get a list of dataframes that contains peptide scores, pvalues, and qvalues across all runs.

Usage

getPeptideScores(
  fileInfo,
  peptides,
  oswMerged = TRUE,
  runType = "DIA_Proteomics",
  context = "global"
)

Arguments

fileInfo	(data-frame) Output of getRunNames function.
peptides	(integer) Ids of peptides for which scores are required.
oswMerged	(logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.
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

(list of dataframes) dataframe has 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

getRunNames, fetchPeptidesInfo

Examples

dataPath <- system.file("extdata", package = "DIAlignR")
fileInfo <- getRunNames(dataPath = dataPath)
precursorsInfo <- getPrecursors(fileInfo, oswMerged = TRUE, runType = "DIA_Proteomics",
context = "experiment-wide", maxPeptideFdr = 0.05)
peptidesInfo <- getPeptideScores(fileInfo, unique(precursorsInfo$peptide_id))
dim(peptidesInfo) # 684 5

Roestlab/DIAlign documentation built on Feb. 25, 2021, 5:18 p.m.