getMultipeptide: Get multipeptides

View source: R/utils.R

getMultipeptideR Documentation

Get multipeptides

Description

Each element of the multipeptide is a collection of features associated with a peptide.

Usage

getMultipeptide(
  precursors,
  features,
  runType = "DIA_Proteomics",
  applyFun = lapply,
  masters = NULL
)

Arguments

precursors

(data-frames) Contains precursors and associated transition IDs.

features

(list of data-frames) Contains features and their properties identified in each run.

runType

(char) This must be one of the strings "DIA_Proteomics", "DIA_IPF", "DIA_Metabolomics".

applyFun

(function) value must be either lapply or BiocParallel::bplapply.

masters

(characters) names of extra runs.

Value

(list) of dataframes having following columns:

transition_group_id

(integer) a unique id for each precursor.

run

(string) run identifier.

RT

(numeric) retention time as in FEATURE.EXP_RT of osw files.

Intensity

(numeric) peak intensity as in FEATURE_MS2.AREA_INTENSITY of osw files.

leftWidth

(numeric) as in FEATURE.LEFT_WIDTH of osw files.

rightWidth

(numeric) as in FEATURE.RIGHT_WIDTH of osw files.

peak_group_rank

(integer) rank of each feature associated with transition_group_id.

m_score

(numeric) q-value of each feature associated with transition_group_id.

alignment_rank

(integer) rank of each feature post-alignment.

Author(s)

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

ORCID: 0000-0003-3500-8152

License: (c) Author (2020) + GPL-3 Date: 2020-04-08

See Also

getPrecursors, getFeatures

Examples

dataPath <- system.file("extdata", package = "DIAlignR")
fileInfo <- getRunNames(dataPath, oswMerged = TRUE)
precursors <- getPrecursors(fileInfo, oswMerged = TRUE, context = "experiment-wide")
features <- getFeatures(fileInfo, maxFdrQuery = 0.05)
multipeptide <- getMultipeptide(precursors, features)
multipeptide[["9861"]]

shubham1637/DIAlign documentation built on March 27, 2023, 7:12 a.m.