getAlignedTimesFast: Get aligned Retention times.

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

Get aligned Retention times.

Description

This function aligns XICs of reference and experiment runs. It produces aligned retention times between refernce run and experiment run.

Usage

getAlignedTimesFast(XICs.ref, XICs.eXp, globalFit, adaptiveRT, params)

Arguments

XICs.ref	List of extracted ion chromatograms from reference run.
XICs.eXp	List of extracted ion chromatograms from experiment run.
globalFit	Linear or loess fit object between reference and experiment run.
adaptiveRT	(numeric) Similarity matrix is not penalized within adaptive RT.
params	(list) parameters are entered as list. Output of the paramsDIAlignR function.

Value

(matrix) the first column corresponds to the aligned reference time, the second column is the aligned experiment time.

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2021) + GPL-3 Date: 2021-01-02

See Also

alignChromatogramsCpp, getAlignObj

Examples

data(XIC_QFNNTDIVLLEDFQK_3_DIAlignR, package="DIAlignR")
data(oswFiles_DIAlignR, package="DIAlignR")
run1 <- "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"
run2 <- "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"
XICs.ref <- lapply(XIC_QFNNTDIVLLEDFQK_3_DIAlignR[[run1]][["4618"]], as.matrix)
XICs.eXp <- lapply(XIC_QFNNTDIVLLEDFQK_3_DIAlignR[[run2]][["4618"]], as.matrix)
params <- paramsDIAlignR()
params[["globalAlignment"]] <- "linear"
globalFit <- getGlobalAlignment(oswFiles_DIAlignR, ref = "run2", eXp = "run0",
 fitType = params[["globalAlignment"]], maxFdrGlobal = 0.05, spanvalue = 0.1)
adaptiveRT <- 77.82315 #3.5*getRSE(globalFit, params[["globalAlignment"]])
globalFit <- coef(globalFit)
getAlignedTimesFast(XICs.ref, XICs.eXp, globalFit, adaptiveRT, params)

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