peakPantheR_ROIStatistics: Save to disk each ROI EIC and mean IS RT

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

Save to disk each ROI EIC and mean IS RT

Description

Using reference samples (referenceSpectraFiles), save (to saveFolder) each ROI EIC (ROI) and reports the mean apex RT for all IS (IS_ROI) across samples

Usage

peakPantheR_ROIStatistics(
    referenceSpectraFiles,
    saveFolder,
    ROI = NULL,
    IS_ROI = NULL,
    sampleColour = NULL,
    ncores = 0,
    saveISPlots = TRUE,
    verbose = TRUE
)

Arguments

referenceSpectraFiles	(str) A character vector of paths to the reference spectra files
saveFolder	(str) Path to the folder where EICs and IS mean RT (IS_mean_RT.csv) will be saved
ROI	(data.frame) NULL or a data.frame of Regions Of Interest (ROI) with compounds as row and ROI parameters as columns: rtMin (float in seconds), rt (float in seconds, or NA), rtMax (float in seconds), mzMin (float), mz (float or NA), mzMax (float) (if NULL, ROI EICs are not saved)
IS_ROI	(data.frame) NULL or a data.frame of IS ROI with IS as row and ROI parameters as columns: rtMin (float in seconds), rt (float in seconds, or NA), rtMax (float in seconds), mzMin (float), mz (float or NA), mzMax (float) (if NULL IS mean RT is not calculated and saved in IS_mean_RT.csv)
sampleColour	(str) NULL or vector colour for each sample
ncores	(int) Number of cores to use to integrate IS in parallel
saveISPlots	(bool) If TRUE save a diagnostic plot for each IS to saveFolder/IS_search compound
verbose	(bool) If TRUE message progress

Value

None

Examples

if(requireNamespace('faahKO')){
## Initialise a peakPantheRAnnotation object with 2 samples and 1 targeted
## compound

# Paths to spectra files
library(faahKO)
spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
                    system.file('cdf/KO/ko16.CDF', package = 'faahKO'))

# targetFeatTable
targetFeatTable <- data.frame(matrix(vector(), 1, 8, dimnames=list(c(),
                    c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
                    'mzMax'))), stringsAsFactors=FALSE)
targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
                        522.2, 522.205222)
targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
                                    FUN.VALUE=numeric(1))

# input
refSpecFiles  <- spectraPaths
input_ROI     <- targetFeatTable
input_IS_ROI  <- targetFeatTable
sampleColour  <- c('blue', 'red')

# temporary saveFolder
saveFolder1   <- tempdir()

# Calculate ROI statiscs
peakPantheR_ROIStatistics(refSpecFiles, saveFolder1, ROI=input_ROI,
                            IS_ROI=input_IS_ROI, sampleColour=sampleColour,
                            ncores=0, saveISPlots=TRUE, verbose=TRUE)
}

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