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

Description Usage Arguments Value Examples

View source: R/peakPantheR_ROIStatistics.R

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

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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

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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)
}

peakPantheR documentation built on April 29, 2020, 5:23 a.m.