groupInfo,ncGTWinput-method {ncGTW} | R Documentation

## ncGTWinput-accessors

### Description

Accessors to the feature and profiles loaded by `loadProfile`.

### Usage

    ## S4 method for signature 'ncGTWinput'
    groupInfo(object)

    ## S4 method for signature 'ncGTWinput'
    profiles(object)

    ## S4 method for signature 'ncGTWinput'
    rtRaw(object)

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

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

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

### Arguments

`object` | a `ncGTWinput` object.

### Value

`groupInfo` returns a vector of the information of the loaded feature.

`profiles` returns a raw data matrix in which each row is a sample profile.

`rtRaw` returns a raw RT matrix in which each row is the corresponding sample RT.

`scanRange` returns a downsampled RT matrix in which each row is the corresponding sample RT in `data`.

`ncGTWpath` returns a list of the same length as the sample number, in which each element is a matrix of the alignment result of the corresponding sample.

`downSample` returns the factor of downsampling when perform ncGTW alignment.

### 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)

    gInfo <- groupInfo(ncGTWinputs[[1]])
    prof <- profiles(ncGTWinputs[[1]])
    rtR <- rtRaw(ncGTWinputs[[1]])

    ## End(Not run)

[Package ncGTW version 1.2.0 Index]