getPrecursors: Get precursors from all feature files

In shubham1637/DIAlign: Dynamic Programming Based Alignment of MS2 Chromatograms

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, [e-mail]

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.