getNativeIDs: Fetch NativeIDs
In shubham1637/DIAlign: Dynamic Programming Based Alignment of MS2 Chromatograms

getNativeIDs

R Documentation

Fetch NativeIDs

Description

Get transition(native) IDs for the peptides.

Usage

getNativeIDs(oswIn, peps, params = paramsDIAlignR(), oswMerged = TRUE)

Arguments

`oswIn`	(string) path to the osw feature file.
`peps`	(integer) ids of peptides to be aligned. If NULL, align all peptides.
`params`	(list) parameters are entered as list. Output of the `paramsDIAlignR` function.
`oswMerged`	(logical) TRUE if merged file from pyprophet is used.

Value

(integer) a vector of transition IDs.

Author(s)

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

ORCID: 0000-0003-3500-8152

License: (c) Author (2022) + GPL-3 Date: 2022-04-19

Examples

dataPath <- system.file("extdata", package = "DIAlignR")
oswIn <- file.path(dataPath, "osw", "merged.osw")
peps <- c(3L, 11L) # No transitions for 3L.
params <- paramsDIAlignR()
params[["context"]] <- "experiment-wide"
getNativeIDs(oswIn, peps, params) # 106468 106469 106470 106471 106472 106473

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