getPrecursors: Get precursors from all feature files

getPrecursorsR Documentation

Get precursors from all feature files

Description

Get a data-frame of analytes' transition_group_id, transition_ids, peptide_id and amino-acid sequences.

Usage

getPrecursors(
  fileInfo,
  oswMerged = TRUE,
  runType = "DIA_Proteomics",
  context = "global",
  maxPeptideFdr = 0.05,
  level = "Peptide",
  useIdentifying = FALSE
)

Arguments

fileInfo

(data-frame) Output of getRunNames function.

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_IPF", "DIA_Metabolomics".

context

(string) Context used in pyprophet peptide. Must be either "run-specific", "experiment-wide", or "global".

maxPeptideFdr

(numeric) A numeric value between 0 and 1. It is used to filter peptides from osw file which have SCORE_PEPTIDE.QVALUE less than itself.

level

(string) Apply maxPeptideFDR on Protein as well if specified as "Protein". Default: "Peptide".

useIdentifying

(logical) Set TRUE to use identifying transitions in alignment. (DEFAULT: FALSE)

Value

(data-frames) A data-frame having following columns:

transition_group_id

(integer) a unique id for each precursor.

peptide_id

(integer) a unique id for each peptide. A peptide can have multiple precursors.

sequence

(string) amino-acid sequence of the precursor with possible modifications.

charge

(integer) charge on the precursor.

group_label

(string) TODO Figure it out.

transition_ids

(list) fragment-ion ID associated with transition_group_id. This is matched with chromatogram ID in mzML file.

Author(s)

Shubham Gupta, shubh.gupta@mail.utoronto.ca

ORCID: 0000-0003-3500-8152

License: (c) Author (2019) + GPL-3 Date: 2019-04-06

See Also

getRunNames, fetchPrecursorsInfo

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)
dim(precursorsInfo) # 234  6

shubham1637/DIAlign documentation built on March 27, 2023, 7:12 a.m.