fetchPrecursorsInfo: Get precursors from a feature file

In DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Description

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

Usage

fetchPrecursorsInfo(filename, runType, selectIDs = NULL)

Arguments

filename	(string) Should be from the RUN.FILENAME column from osw files.
runType	(string) This must be one of the strings "DIA_proteomics", "DIA_Metabolomics".

Value

(data-frames) Data-frame has 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, [e-mail]

ORCID: 0000-0003-3500-8152

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

See Also

getRunNames, getPrecursors, getPrecursorsQuery

Examples

dataPath <- system.file("extdata", package = "DIAlignR")
filename <- paste0(dataPath,"/osw/merged.osw")
## Not run: 
precursorsInfo <- fetchPrecursorsInfo(filename, runType = "DIA_proteomics")
dim(precursorsInfo) # 303  6

## End(Not run)

DIAlignR documentation built on Nov. 8, 2020, 8:22 p.m.