alignData,ncGTWoutput-method {ncGTW} | R Documentation

## ncGTWoutput-accessors

### Description

Accessors to the alignment information and result by ncGTW.

### Usage

    ## S4 method for signature 'ncGTWoutput'
    alignData(object)

### Arguments

`object` | a `ncGTWoutput` object.

### Value

`alignData` returns a matrix in which each row is a sample profile after downsampling.

### 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 <- initncGTWparam()

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

    data <- alignData(ncGTWoutputs[[1]])
    rt <- scanRange(ncGTWoutputs[[1]])
    paths <- ncGTWpath(ncGTWoutputs[[1]])
    downSam <- downSample(ncGTWoutputs[[1]])

    ## End(Not run)

[Package ncGTW version 1.2.0 Index]