getMultipeptide: Get multipeptides

In Roestlab/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Description

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

Usage

getMultipeptide(
  precursors,
  features,
  applyFun = lapply,
  numMerge = 0L,
  startIdx = 0L
)

Arguments

precursors	(data-frames) Contains precursors and associated transition IDs.
features	(list of data-frames) Contains features and their properties identified in each run.
applyFun	(function) value must be either lapply or BiocParallel::bplapply.
numMerge	(integer) number of merged runs. Should be 0 for star alignment.
startIdx	(integer) suffix for merged runs' name.

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, [e-mail]

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"]]

Roestlab/DIAlignR documentation built on March 3, 2021, 9:09 a.m.