getNativeIDs: Fetch NativeIDs

In shubham1637/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

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, [e-mail]

ORCID: 0000-0003-3500-8152

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

See Also

reduceXICs

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/DIAlignR documentation built on March 29, 2023, 8:45 p.m.