load_annotation_from_file_UI_helper: UI data import helper - check loaded annotation

In phenomecentre/peakPantheR: Peak Picking and Annotation of High Resolution Experiments

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

phenomecentre/peakPantheR documentation built on Feb. 29, 2024, 9:07 p.m.