initialise_annotation_from_files_UI_helper: UI data import helper - initialise new annotation from files

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

UI data import helper - initialise new annotation from files

Description

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

Usage

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

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