peakPantheRAnnotation: An S4 class to represent peakPantheR annotation results

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

An S4 class to represent peakPantheR annotation results

Description

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.

Usage

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 = FALSE),
    FIR = data.frame(rtMin = numeric(), rtMax = numeric(), mzMin =
    numeric(), mzMax = numeric(), stringsAsFactors = FALSE),
    uROI = data.frame(rtMin = numeric(), rt = numeric(), rtMax = numeric(),
    mzMin = numeric(), mz = numeric(), mzMax = numeric(), stringsAsFactors =
    FALSE), 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 = FALSE),
    FIR = data.frame(rtMin = numeric(), rtMax = numeric(), mzMin =
    numeric(), mzMax = numeric(), stringsAsFactors = FALSE),
    uROI = data.frame(rtMin = numeric(), rt = numeric(), rtMax = numeric(),
    mzMin = numeric(), mz = numeric(), mzMax = numeric(), stringsAsFactors =
    FALSE), 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)

Arguments

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

Details

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.

Value

(peakPantheRAnnotation)

Slots

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
peakAreaRaw	integrated peak area from raw data points
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

See Also

Other peakPantheR: peakPantheR_parallelAnnotation(), peakPantheR_singleFileSearch()

Other parallelAnnotation: peakPantheR_parallelAnnotation(), peakPantheR_singleFileSearch()

Examples

if(requireNamespace('faahKO')){
## 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=FALSE)
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)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
                                    FUN.VALUE=numeric(2))

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'
# [6] 'filepath'    'cpdMetadata'  'spectraMetadata' 'acquisitionTime'
# [10] 'uROIExist'  'useUROI'      'useFIR'          'TIC'       'peakTables'
# [15] 'dataPoints' 'peakFit'      'isAnnotated'

## Slots shouldn't be accessed directly, accessors are available:
cpdID(annotation)
# [1] 'ID-1' 'ID-2'
cpdName(annotation)
# [1] 'Cpd 1' 'Cpd 2'
ROI(annotation)
#   rtMin       rt rtMax    mzMin    mz    mzMax cpdID cpdName
# 1  3310 3344.888  3390 522.1948 522.2 522.2052  ID-1   Cpd 1
# 2  3280 3385.577  3440 496.1950 496.2 496.2050  ID-2   Cpd 2
FIR(annotation)
#   rtMin rtMax mzMin mzMax cpdID cpdName
# 1    NA    NA    NA    NA  ID-1   Cpd 1
# 2    NA    NA    NA    NA  ID-2   Cpd 2
uROI(annotation)
#   rtMin rt rtMax mzMin mz mzMax cpdID cpdName
# 1    NA NA    NA    NA NA    NA  ID-1   Cpd 1
# 2    NA NA    NA    NA NA    NA  ID-2   Cpd 2
filepath(annotation)
# [1] 'C:/R/R-3.6.0/library/faahKO/cdf/KO/ko15.CDF'
# [2]'C:/R/R-3.6.0/library/faahKO/cdf/KO/ko16.CDF'
# [3] 'C:/R/R-3.6.0/library/faahKO/cdf/KO/ko18.CDF'
cpdMetadata(annotation)
# data frame with 0 columns and 2 rows
spectraMetadata(annotation)
# data frame with 0 columns and 3 rows
acquisitionTime(annotation)
# [1] NA NA NA
uROIExist(annotation)
# [1] FALSE
useUROI(annotation)
# [1] FALSE
useFIR(annotation)
# [1] FALSE
TIC(annotation)
# [1] NA NA NA
peakTables(annotation)
# [[1]]
# NULL
# [[2]]
# NULL
# [[3]]
# NULL
dataPoints(annotation)
# [[1]]
# NULL
# [[2]]
# NULL
# [[3]]
# NULL
peakFit(annotation)
# [[1]]
# NULL
# [[2]]
# NULL
# [[3]]
# NULL
isAnnotated(annotation)
# [1] FALSE
}

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