getPrecursorByID: Find precursors given their IDs

getPrecursorByIDR Documentation

Find precursors given their IDs

Description

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

Usage

getPrecursorByID(
  analytes,
  fileInfo,
  oswMerged = TRUE,
  runType = "DIA_Proteomics"
)

Arguments

analytes

(integer) a vector of integers.

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".

Value

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

transition_group_id

(integer) a unique id for each precursor.

transition_id

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

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.

Author(s)

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

ORCID: 0000-0003-3500-8152

License: (c) Author (2020) + GPL-3 Date: 2019-04-06

See Also

getRunNames, fetchPrecursorsInfo

Examples

dataPath <- system.file("extdata", package = "DIAlignR")
fileInfo <- getRunNames(dataPath = dataPath, oswMerged = TRUE)
precursors <- getPrecursorByID(c(32L, 2474L), fileInfo, oswMerged = TRUE)

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