peakPantheR_loadAnnotationParamsCSV {peakPantheR} | R Documentation

## Load fit parameters from CSV

### Description

Initialise a new `peakPantheRAnnotation` object after loading ROI, uROI and FIR parameters from CSV. `spectraPaths`, `spectraMetadata` or `cpdMetadata` are not initialised and will need to be filled before annotation. `useUROI` and `useFIR` are set to `FALSE` and will need to be set accordingly. `uROIExist` is established depending on the uROI columns present in the CSV and will be set to `TRUE` only if no `NA` are present

### Usage

    peakPantheR_loadAnnotationParamsCSV(CSVParamPath, verbose = TRUE)

### Arguments

`CSVParamPath` | (str) Path to a CSV file of fit parameters (e.g. as saved by `outputAnnotationDiagnostic`)
`verbose` | (bool) If TRUE message progress

### Value

(peakPantheRAnnotation) Object initialised with ROI, uROI and FIR read from the CSV file

### Examples

    ## Input data
    input_CSV <- data.frame(matrix(nrow=2,ncol=21,dimnames=list(c(),
        c('cpdID', 'cpdName',
        'X','ROI_rt', 'ROI_mz', 'ROI_rtMin', 'ROI_rtMax','ROI_mzMin','ROI_mzMax',
        'X','uROI_rtMin', 'uROI_rtMax', 'uROI_mzMin', 'uROI_mzMax', 'uROI_rt',
        'uROI_mz', 'X', 'FIR_rtMin', 'FIR_rtMax', 'FIR_mzMin', 'FIR_mzMax'))))
    input_CSV[1,]  <- c('ID-1', 'Cpd 1', '|', 1.,  2.,  3.,  4.,  5.,  6.,  '|',
                        7.,  8.,  9.,  10., 11., 12., '|', 13., 14., 15., 16.)
    input_CSV[2,]  <- c('ID-2', 'Cpd 2', '|', 17., 18., 19., 20., 21., 22., '|',
                        23., 24., 25., 26., 27., 28., '|', 29., 30., 31., 32.)
    input_CSV[,-c(1,2,3,10,17)]  <- vapply(input_CSV[,-c(1,2,3,10,17)],
                                                as.numeric, FUN.VALUE=numeric(2))

    # temporary file location
    savePath1      <- tempfile(pattern='file', tmpdir=tempdir(), fileext='.csv')
    # save csv
    utils::write.csv(input_CSV, file=savePath1, row.names=FALSE)

    # Load parameters from CSV
    loadedAnnotation <- peakPantheR_loadAnnotationParamsCSV(savePath1,
                                                            verbose=TRUE)
    # uROIExist set to TRUE
    # New peakPantheRAnnotation object initialised for 2 compounds
    # An object of class peakPantheRAnnotation
    #  2 compounds in 0 samples.
    #   updated ROI 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]