getPrecursors {DIAlignR} | R Documentation

## Get precursors from all feature files

### 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",
      context = "global",
      maxPeptideFdr = 0.05,
      level = "Peptide",
      useIdentifying = FALSE
    )

### Arguments

`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".
`context` | (string) Context used in pyprophet peptide. Must be either "run-specific", "experiment-wide", or "global".
`maxPeptideFdr` | (numeric) A numeric value between 0 and 1. It is used to filter peptides from osw file which have SCORE_PEPTIDE.QVALUE less than itself.
`level` | (string) Apply maxPeptideFDR on Protein as well if specified as "Protein". Default: "Peptide".
`useIdentifying` | (logical) Set TRUE to use identifying transitions in alignment. (DEFAULT: FALSE)

### Value

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

`transition_group_id` | (integer) a unique id for each precursor.
`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.
`transition_ids` | (list) fragment-ion ID associated with transition_group_id. This is matched with chromatogram ID in mzML file.

### Author(s)

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

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 <- getRunNames(dataPath = dataPath)
    precursorsInfo <- getPrecursors(fileInfo, oswMerged = TRUE, runType = "DIA_Proteomics",
    context = "experiment-wide", maxPeptideFdr = 0.05)
    dim(precursorsInfo) # 234  6

[Package DIAlignR version 2.2.0 Index]