load_annotation_from_file_UI_helper {peakPantheR} | R Documentation

## UI data import helper - check loaded annotation

### Description

Load a .RData file (check it exists) and that a peakPantheRAnnotation named "annotationObject" is present. Returns the annotation if everything is valid

### Usage

    load_annotation_from_file_UI_helper(annotationPath)

### Arguments

`annotationPath` | (str) Path to a RData file containing a peakPantheRAnnotation names 'annotationObject'

### Value

(peakPantheRAnnotation) Object loaded from file

### Examples

    ## Initialise a peakPantheRAnnotation object with 3 samples and 2 compounds

    ## Inputs
    # spectraPaths
    spectraPaths <- c('./path/file1', './path/file2', './path/file3')

    # targetFeatTable
    targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
                        c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
                        'mzMax'))), stringsAsFactors=FALSE)
    targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
                            522.2, 522.205222)
    targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
                            496.2, 496.204962)
    targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
                                        FUN.VALUE=numeric(2))

    annotationObject <- peakPantheRAnnotation(spectraPaths=spectraPaths,
                                            targetFeatTable=targetFeatTable)

    # save annotation to disk
    annotPath <- tempfile(pattern="file", tmpdir=tempdir(), fileext='.RData')
    save(annotationObject, file=annotPath, compress=TRUE)

    # Load annotation
    load_annotation_from_file_UI_helper(annotationPath = annotPath)
    # An object of class peakPantheRAnnotation
    #   2 compounds in 3 samples.
    #   updated ROI do not exist (uROI)
    #   does not use updated ROI (uROI)
    #   does not use fallback integration regions (FIR)
    #   is not annotated

[Package peakPantheR version 1.4.0 Index]