getPrecursorByID {DIAlignR} | R 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` | (string) 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, 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)

[Package DIAlignR version 1.2.0 Index]