peakPantheRAnnotation: An S4 class to represent peakPantheR annotation results
In peakPantheR: Peak Picking and Annotation of High Resolution Experiments

Description Usage Arguments Details Slots See Also Examples

View source: R/initialize_peakPantheRAnnotation.R

The peakPantheRAnnotation class is designed to run and store peakPantheR parallel annotation results. Instances of the class are created with the peakPantheRAnnotation constructor function, which initialises an object of proper dimension with spectraPaths (set samples to process) and targetFeatTable (set compounds to target). spectraPaths is a character vector of spectra file paths. targetFeatTable is a data.frame of compounds to target as rows and parameters as columns: cpdID (int), cpdName (str), rtMin (float in seconds), rt (float in seconds, or NA), rtMax (float in seconds), mzMin (float), mz (float or NA), mzMax (float).

peakPantheRAnnotation(): create an instance of the peakPantherAnnotation class.

peakPantheRAnnotation(spectraPaths = NULL, targetFeatTable = NULL,
  cpdID = character(), cpdName = character(), ROI = data.frame(rtMin =
  numeric(), rt = numeric(), rtMax = numeric(), mzMin = numeric(), mz =
  numeric(), mzMax = numeric(), stringsAsFactors = F), FIR = data.frame(rtMin
  = numeric(), rtMax = numeric(), mzMin = numeric(), mzMax = numeric(),
  stringsAsFactors = F), uROI = data.frame(rtMin = numeric(), rt = numeric(),
  rtMax = numeric(), mzMin = numeric(), mz = numeric(), mzMax = numeric(),
  stringsAsFactors = F), filepath = character(), cpdMetadata = data.frame(),
  spectraMetadata = data.frame(), acquisitionTime = character(),
  uROIExist = FALSE, useUROI = FALSE, useFIR = FALSE, TIC = numeric(),
  peakTables = list(), dataPoints = list(), peakFit = list(),
  isAnnotated = FALSE)

peakPantheRAnnotation(spectraPaths = NULL, targetFeatTable = NULL,
  cpdID = character(), cpdName = character(), ROI = data.frame(rtMin =
  numeric(), rt = numeric(), rtMax = numeric(), mzMin = numeric(), mz =
  numeric(), mzMax = numeric(), stringsAsFactors = F), FIR = data.frame(rtMin
  = numeric(), rtMax = numeric(), mzMin = numeric(), mzMax = numeric(),
  stringsAsFactors = F), uROI = data.frame(rtMin = numeric(), rt = numeric(),
  rtMax = numeric(), mzMin = numeric(), mz = numeric(), mzMax = numeric(),
  stringsAsFactors = F), filepath = character(), cpdMetadata = data.frame(),
  spectraMetadata = data.frame(), acquisitionTime = character(),
  uROIExist = FALSE, useUROI = FALSE, useFIR = FALSE, TIC = numeric(),
  peakTables = list(), dataPoints = list(), peakFit = list(),
  isAnnotated = FALSE)

`spectraPaths`	NULL or a character vector of spectra file paths, to set samples to process
`targetFeatTable`	NULL or a `data.frame` of compounds to target as rows and parameters as columns: `cpdID` (str), `cpdName` (str), `rtMin` (float in seconds), `rt` (float in seconds, or NA), `rtMax` (float in seconds), `mzMin` (float), `mz` (float or NA), `mzMax` (float). Set compounds to target.
`cpdID`	A character vector of compound IDs, of length number of compounds
`cpdName`	A character vector of compound names, of length number of compounds
`ROI`	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).
`FIR`	A data.frame of Fallback Integration Regions (FIR) with compounds as row and FIR parameters as columns: `rtMin` (float in seconds), `rtMax` (float in seconds), `mzMin` (float), `mzMax` (float).
`uROI`	A data.frame of updated Regions Of Interest (uROI) with compounds as row and uROI 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).
`filepath`	A character vector of file paths, of length number of spectra files
`cpdMetadata`	A data.frame of compound metadata, with compounds as row and metadata as columns
`spectraMetadata`	A data.frame of sample metadata, with samples as row and metadata as columns
`acquisitionTime`	A character vector of acquisition date-time (converted from POSIXct) or NA
`uROIExist`	A logical stating if uROI have been set
`useUROI`	A logical stating if uROI are to be used
`useFIR`	A logical stating if FIR are to be used
`TIC`	A numeric vector of TIC or NA, of length number of spectra files
`peakTables`	A list of peakTable data.frame, of length number of spectra files. Each peakTable data.frame has compounds as rows and peak annotation results as columns.
`dataPoints`	A list of length number of spectra files. Each list element is a ROIsDataPoint list of `data.frame` of raw data points for each ROI/uROI (retention time "rt", mass "mz" and intensity "int" (as column) of each raw data points (as row))
`peakFit`	A list of length number of spectra files. Each list element is a curveFit list of `peakPantheR_curveFit` or NA for each ROI
`isAnnotated`	A logical stating in the annotation took place

The validObject method ensures the conformity of an object to the peakPantheRAnnotation-class. The number of compounds is based on @cpdID length, and the number of samples is based on @filepath length. Slot type is not checked as setClass enforces it. peakTables and EICs type are checked on the first list element. annotationTable(object, column) where column is a column from peakTable, returns a data.frame of values with the samples as rows, ROI as columns.

cpdID

A character vector of compound IDs, of length number of compounds

cpdName

A character vector of compound names, of length number of compounds

ROI

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).

FIR

A data.frame of Fallback Integration Regions (FIR) with compounds as row and FIR parameters as columns: rtMin (float in seconds), rtMax (float in seconds), mzMin (float), mzMax (float).

uROI

A data.frame of updated Regions Of Interest (uROI) with compounds as row and uROI 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).

filepath

A character vector of file paths, of length number of spectra files

cpdMetadata

A data.frame of compound metadata, with compounds as row and metadata as columns

spectraMetadata

A data.frame of sample metadata, with samples as row and metadata as columns

acquisitionTime

A character vector of acquisition date-time (converted from POSIXct) or NA

uROIExist

A logical stating if uROI have been set

useUROI

A logical stating if uROI are to be used

useFIR

A logical stating if FIR are to be used

TIC

A numeric vector of TIC or NA, of length number of spectra files

peakTables

A list of peakTable data.frame, of length number of spectra files. Each peakTable data.frame has compounds as rows and peak annotation results as columns.

dataPoints

A list of length number of spectra files. Each list element is a ROIsDataPoint list of data.frame of raw data points for each ROI/uROI (retention time "rt", mass "mz" and intensity "int" (as column) of each raw data points (as row))

peakFit

A list of length number of spectra files. Each list element is a curveFit list of peakPantheR_curveFit or NA for each ROI

isAnnotated

A logical stating if the annotation has taken place

Details:

The peakTables data.frame are structured as follow:

cpdID	database compound ID
cpdName	compound name
found	was the peak found
rt	retention time of peak apex (sec)
rtMin	leading edge of peak retention time (sec) determined at 0.5% of apex intensity
rtMax	trailing edge of peak retention time (sec) determined at 0.5% of apex intensity
mz	weighted (by intensity) mean of peak m/z across scans
mzMin	m/z peak minimum (between rtMin, rtMax)
mzMax	m/z peak maximum (between rtMin, rtMax)
peakArea	integrated peak area
maxIntMeasured	maximum peak intensity in raw data
maxIntPredicted	maximum peak intensity based on curve fit
is_filled	Logical indicate if the feature was integrated using FIR (Fallback Integration Region)
ppm_error	difference in ppm between the expected and measured m/z
rt_dev_sec	difference in seconds between the expected and measured rt
tailingFactor	the tailing factor is a measure of peak tailing.It is defined as the distance from the front slope of the peak to the back slope divided by twice the distance from the center line of the peak to the front slope, with all measurements made at 5% of the maximum peak height. The tailing factor of a peak will typically be similar to the asymmetry factor for the same peak, but the two values cannot be directly converted
asymmetryFactor	the asymmetry factor is a measure of peak tailing. It is defined as the distance from the center line of the peak to the back slope divided by the distance from the center line of the peak to the front slope, with all measurements made at 10% of the maximum peak height. The asymmetry factor of a peak will typically be similar to the tailing factor for the same peak, but the two values cannot be directly converted

Other peakPantheR: peakPantheR_parallelAnnotation, peakPantheR_singleFileSearch

Other parallelAnnotation: peakPantheR_parallelAnnotation, peakPantheR_singleFileSearch

if(requireNamespace("faahKO") & getRversion()<"3.6"){
## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted compounds

# Paths to spectra files
library(faahKO)
spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
                  system.file('cdf/KO/ko16.CDF', package = "faahKO"),
                  system.file('cdf/KO/ko18.CDF', package = "faahKO"))

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

annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths, targetFeatTable=targetFeatTable)

annotation
# An object of class peakPantheRAnnotation
#  2 compounds in 3 samples.
#   updated ROI do not exist (uROI)
#   does not use updated ROI (uROI)
#   does not use fallback integration regions (FIR)
#   is not annotated

slotNames(annotation)
# [1] "cpdID"       "cpdName"         "ROI"             "FIR"       "uROI"        "filepath"       
# [7] "cpdMetadata" "spectraMetadata" "acquisitionTime" "uROIExist" "useUROI"     "useFIR"         
# [13] "TIC"        "peakTables"      "dataPoints"      "peakFit"   "isAnnotated"

annotation@cpdID
# [1] "ID-1" "ID-2"
annotation@cpdName
# [1] "Cpd 1" "Cpd 2"
annotation@ROI
#   rtMin       rt rtMax    mzMin    mz    mzMax
# 1  3310 3344.888  3390 522.1948 522.2 522.2052
# 2  3280 3385.577  3440 496.1950 496.2 496.2050
annotation@FIR
#   rtMin rtMax mzMin mzMax
# 1    NA    NA    NA    NA
# 2    NA    NA    NA    NA
annotation@uROI
#   rtMin rt rtMax mzMin mz mzMax
# 1    NA NA    NA    NA NA    NA
# 2    NA NA    NA    NA NA    NA
annotation@filepath
# [1] "C:/R/R-3.4.3/library/faahKO/cdf/KO/ko15.CDF" "C:/R/R-3.4.3/library/faahKO/cdf/KO/ko16.CDF"
# [2] "C:/R/R-3.4.3/library/faahKO/cdf/KO/ko18.CDF"
annotation@cpdMetadata
# data frame with 0 columns and 2 rows
annotation@spectraMetadata
# data frame with 0 columns and 3 rows
annotation@acquisitionTime
# [1] NA NA NA
annotation@uROIExist
# [1] FALSE
annotation@useUROI
# [1] FALSE
annotation@useFIR
# [1] FALSE
annotation@TIC
# [1] NA NA NA
annotation@peakTables
# [[1]]
# NULL
# [[2]]
# NULL
# [[3]]
# NULL
annotation@dataPoints
# [[1]]
# NULL
# [[2]]
# NULL
# [[3]]
# NULL
annotation@peakFit
# [[1]]
# NULL
# [[2]]
# NULL
# [[3]]
# NULL
annotation@isAnnotated
# [1] FALSE
}