getPeptideScores: Get scores of peptide

Description Usage Arguments Value Author(s) See Also Examples

Description

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

Usage

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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, shubh.gupta@mail.utoronto.ca

ORCID: 0000-0003-3500-8152

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

See Also

getRunNames, fetchPeptidesInfo

Examples

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