initialise_annotation_from_files_UI_helper {peakPantheR} | R Documentation |
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 )
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 |
(peakPantheRAnnotation) Object initialised with ROI, uROI and FIR read from the CSV file
## 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