Real Time Annotation"

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
if (getRversion() >= "3.6") {
  knitr::opts_chunk$set(eval = FALSE)
}
required <- c("faahKO")
if (!all(unlist(lapply(required, function(pkg) requireNamespace(pkg, quietly = TRUE))))) {
  knitr::opts_chunk$set(eval = FALSE)
}

The peakPantheR package is designed for the detection, integration and reporting of pre-defined features in MS files.

The Real Time Annotation is set to detect and integrate multiple compounds in one file at a time.

Using an example dataset, this vignette will:

Real Time Annotation Concept

Real time compound integration is set to:

Real Time Annotation Example

We can target two features in a MS spectra file from the faahKO package with peakPantheR_singleFileSearch():

setRepositories(ind=1:4)
install.packages('faahKO')

Input Data

An input spectra is selected:

# hide package load message
library(faahKO)
library(faahKO)
## file paths
input_spectraPath  <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"))
input_spectraPath

Two targeed features are defined and stored in a table with as columns:

# targetFeatTable
input_targetFeatTable     <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(), c("cpdID", "cpdName", "rtMin", "rt", "rtMax", "mzMin", "mz", "mzMax"))), stringsAsFactors=F)
input_targetFeatTable[1,] <- c("ID-1", "Cpd 1", 3310., 3344.888, 3390., 522.194778, 522.2, 522.205222)
input_targetFeatTable[2,] <- c("ID-2", "Cpd 2", 3280., 3385.577, 3440., 496.195038, 496.2, 496.204962)
input_targetFeatTable[,c(3:8)] <- sapply(input_targetFeatTable[,c(3:8)], as.numeric)
input_targetFeatTable     <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(), c("cpdID", "cpdName", "rtMin", "rt", "rtMax", "mzMin", "mz", "mzMax"))), stringsAsFactors=F)
input_targetFeatTable[1,] <- c("ID-1", "Cpd 1", 3310., 3344.888, 3390., 522.194778, 522.2, 522.205222)
input_targetFeatTable[2,] <- c("ID-2", "Cpd 2", 3280., 3385.577, 3440., 496.195038, 496.2, 496.204962)
input_targetFeatTable[,c(3:8)] <- sapply(input_targetFeatTable[,c(3:8)], as.numeric)
rownames(input_targetFeatTable) <- NULL
pander::pandoc.table(input_targetFeatTable, digits = 9)

Run Single File Annotation

peakPantheR_singleFileSearch() takes as input a singleSpectraDataPath pointing to the file to process and targetFeatTable defining the compounds to integrate:

library(peakPantheR)
annotation <- peakPantheR_singleFileSearch(singleSpectraDataPath = input_spectraPath,
                                           targetFeatTable = input_targetFeatTable,
                                           peakStatistic = TRUE,
                                           verbose = TRUE)
annotation$TIC
annotation$acquTime
annotation$peakTable
pander::pandoc.table(annotation$peakTable, digits = 7)
annotation$curveFit
annotation$ROIsDataPoint

Multiple parameters control the file annotation:

The summary plot generated by plotEICsPath, corresponding to the EICs of each integrated regions of interest is as follow:

knitr::include_graphics("../man/figures/singleFileSearch_EICsPlot.png")

EICs plot: Each panel correspond to a targeted feature, with the EIC extracted on the mzMin, mzMax range found. The red dot marks the RT peak apex, and the red line highlights the RT peakwidth range found (rtMin, rtMax)

See Also



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peakPantheR documentation built on May 1, 2019, 10:53 p.m.