UI data import helper - initialise new annotation from files — initialise_annotation_from_files_UI

Fully initialise a peakPantheRAnnotation using the target files path, CSV parameter path and metadata.

initialise_annotation_from_files_UI_helper(
    CSVParamPath,
    spectraPaths,
    cpdMetadataPath = NULL,
    spectraMetadata = NULL,
    verbose = TRUE
)

Arguments

CSVParamPath: (str) Path to a CSV file of fit parameters
spectraPaths: (str) character vector of spectra file paths, to set samples to process
cpdMetadataPath: NULL or path to a csv of compound metadata, with compounds as row and metadata as columns
spectraMetadata: NULL or DataFrame of sample metadata, with samples as row and metadata as columns
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))

input_spectraPaths    <- c('./path/file1', './path/file2', './path/file3')

# 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 <- initialise_annotation_from_files_UI_helper(savePath1,
                                                        input_spectraPaths,
                                                        verbose=TRUE)
#> An object of class peakPantheRAnnotation
#>  2 compounds in 3 samples. 
#>   updated ROI exist (uROI)
#>   does not use updated ROI (uROI)
#>   does not use fallback integration regions (FIR)
#>   is not annotated
#> 
# An object of class peakPantheRAnnotation
#   2 compounds in 3 samples.
#   updated ROI exist (uROI)
#   does not use updated ROI (uROI)
#   does not use fallback integration regions (FIR)
#   is not annotated