peakPantheR_loadAnnotationParamsCSV: Load fit parameters from CSV

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

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

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