fetchPrecursorsInfo {DIAlignR} | R Documentation

## Get precursors from a feature file

### 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, shubh.gupta@mail.utoronto.ca

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)

[Package DIAlignR version 1.2.0 Index]