addXIC: Add XIC to pyopenms experiment

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

Description

A chromatogram and its repective native ID (transition ID) is added to MSExperiment object.

Usage

addXIC(ropenms, expriment, xic, nativeId)

Arguments

ropenms	(pyopenms module) get this python module through get_ropenms().
expriment	(python object) an MSExperiment() created using ropenms.
xic	(data-frame) must have two numeric columns.
nativeId	(integer) transition ID of the xic.

Value

(None)

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2020) + GPL-3 Date: 2020-06-06

Examples

## Not run: 
ropenms <- get_ropenms(condaEnv = "envName", useConda=TRUE)
expriment <- ropenms$MSExperiment()
data(XIC_QFNNTDIVLLEDFQK_3_DIAlignR)
xic <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR[["hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"]][["4618"]][[1]]
addXIC(ropenms, expriment, xic, 34L)
chroms <- expriment$getChromatograms()
reticulate::py_to_r(chroms[[0]]$getNativeID())
reticulate::py_to_r(chroms[[0]]$get_peaks())

## End(Not run)

Roestlab/DIAlign documentation built on Feb. 25, 2021, 5:18 p.m.