setAlignmentRank {DIAlignR} | R Documentation

## Set Alignment rank to the aligned feature

### Description

Picks the top feature in run by comparing m-score to unaligned FDR and aligned FDR. If no satisfactory feature is found, peak-integration is carried out by mapping left and right peak boundaries from the reference feature and integrating area under the curve.

### Usage

    setAlignmentRank(df, refIdx, eXp, tAligned, XICs, params, adaptiveRT)

### Arguments

`df` | (dataframe) a collection of features related to the peptide
`refIdx` | (integer) index of the reference feature in df.
`eXp` | (string) name of the run to be aligned to reference run. Must be in the rownames of fileInfo.
`tAligned` | (list) the first element corresponds to the aligned reference time, the second element is the aligned experiment time.
`XICs` | (list of dataframes) fragment-ion chromatograms of the analytes for all runs.
`params` | (list) parameters are entered as list. Output of the `paramsDIAlignR` function.
`adaptiveRT` | (numeric) defines the window around the aligned retention time, within which features with m-score below aligned FDR are considered for quantification.
`XICs.eXp` | (list) list of extracted ion chromatograms from experiment run.

### Value

invisible NULL

### Author(s)

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

ORCID: 0000-0003-3500-8152

License: (c) Author (2020) + GPL-3 Date: 2020-04-13

### See Also

`getMultipeptide, calculateIntensity, alignToRef`

### Examples

    data(multipeptide_DIAlignR, package="DIAlignR")
    data(XIC_QFNNTDIVLLEDFQK_3_DIAlignR, package="DIAlignR")
    params <- paramsDIAlignR()
    df <- multipeptide_DIAlignR[["14383"]]
    df$alignment_rank[2] <- 1L
    XICs.ref <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR[["hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]]
    XICs.eXp <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR[["hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]]
    ## Not run:
    # Use getAlignedTimes() to get tAligned.
    alignObj <- testAlignObj()
    tAligned <- alignedTimes2(alignObj, XICs.ref, XICs.eXp)
    setAlignmentRank(df, refIdx = 3L, eXp = "run2", tAligned, XICs.eXp,
    params, adaptiveRT = 38.66)

    ## End(Not run)

[Package DIAlignR version 2.2.0 Index]