getPrecursors: Get precursors from all feature files

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

getPrecursors(fileInfo, oswMerged = TRUE, runType = "DIA_proteomics")

Arguments

fileInfo	(data-frame) Output of DIAlignR::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_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, [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 <- DIAlignR::getRunNames(dataPath = dataPath)
## Not run: 
precursorsInfo <- getPrecursors(fileInfo, oswMerged = TRUE, runType = "DIA_proteomics")
dim(precursorsInfo) # 322  6

## End(Not run)

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