getAlignedTimesFast {DIAlignR} | R Documentation

## 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, shubh.gupta@mail.utoronto.ca

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)

[Package DIAlignR version 2.2.0 Index]