ncGTWalign {ncGTW} | R Documentation

## Run ncGTW alignment

### Description

This function applies ncGTW alignment to the input feature.

### Usage

    ncGTWalign(ncGTWinput, xcmsLargeWin, parSamp = 10, k1Num = 3,
      k2Num = 1, bpParam = BiocParallel::SnowParam(workers = 1),
      ncGTWparam = NULL)

### Arguments

`ncGTWinput` | A `ncGTWinput` object.
`xcmsLargeWin` | A `xcmsSet-class` object.
`parSamp` | Decide how many samples are in each group when considering parallel computing, and the default is 10.
`k1Num` | Decide how many different k1 will be tested in stage 1. The default is 3.
`k2Num` | Decide how many different k2 will be tested in stage 2. The default is 1.
`bpParam` | A object of BiocParallel to control parallel processing, and can be created by `SerialParam`, `MulticoreParam`, or `SnowParam`.
`ncGTWparam` | A `ncGTWparam` object.

### Details

This function realign the input feature with ncGTW alignment function with given m/z and RT range.

### Value

A `ncGTWoutput` object.

### Examples

    # obtain data
    data('xcmsExamples')
    xcmsLargeWin <- xcmsExamples$xcmsLargeWin
    xcmsSmallWin <- xcmsExamples$xcmsSmallWin
    ppm <- xcmsExamples$ppm

    # detect misaligned features
    excluGroups <- misalignDetect(xcmsLargeWin, xcmsSmallWin, ppm)

    # obtain the paths of the sample files
    filepath <- system.file("extdata", package = "ncGTW")
    file <- list.files(filepath, pattern="mzxml", full.names=TRUE)

    tempInd <- matrix(0, length(file), 1)
    for (n in seq_along(file)){
        tempCha <- file[n]
        tempLen <- nchar(tempCha)
        tempInd[n] <- as.numeric(substr(tempCha, regexpr("example", tempCha) + 7,
            tempLen - 6))
    }
    # sort the paths by data acquisition order
    file <- file[sort.int(tempInd, index.return = TRUE)$ix]
    ## Not run:
    # load the sample profiles
    ncGTWinputs <- loadProfile(file, excluGroups)

    # initialize the parameters of ncGTW alignment with default
    ncGTWparam <- new("ncGTWparam")

    # run ncGTW alignment
    ncGTWoutputs <- vector('list', length(ncGTWinputs))
    for (n in seq_along(ncGTWinputs))
        ncGTWoutputs[[n]] <- ncGTWalign(ncGTWinputs[[n]], xcmsLargeWin, 5,
            ncGTWparam = ncGTWparam)

    ## End(Not run)

[Package ncGTW version 1.2.0 Index]