peakPantheRAnnotation: An S4 class to represent peakPantheR annotation results
In peakPantheR: Peak Picking and Annotation of High Resolution Experiments
Description
Usage
Arguments
Details
Value
Slots
See Also
Examples
View source: R/initialize_peakPantheRAnnotation.R
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
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
cpdIDA character vector of compound IDs, of length
number of compounds
cpdNameA character vector of compound names, of length number of
compounds
ROIA 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).
FIRA 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).
uROIA 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).
filepathA character vector of file paths, of
length number of spectra
files
cpdMetadataA data.frame of compound metadata,
with compounds as row and metadata as columns
spectraMetadataA data.frame of sample metadata,
with samples as row and metadata as columns
acquisitionTimeA character
vector of acquisition date-time (converted from POSIXct) or NA
uROIExistA logical stating if uROI have been set
useUROIA logical stating if uROI are to be used
useFIRA logical stating if FIR are to be used
TICA numeric vector of TIC or NA,
of length number of spectra files
peakTablesA 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.
dataPointsA 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))
peakFitA list of length number of spectra files.
Each list element is a curveFit list of
peakPantheR_curveFit or NA for each ROI
isAnnotatedA 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
See Also
Other peakPantheR:
peakPantheR_parallelAnnotation(),
peakPantheR_singleFileSearch()
Other parallelAnnotation:
peakPantheR_parallelAnnotation(),
peakPantheR_singleFileSearch()
Examples
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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
}
peakPantheR documentation built on Nov. 8, 2020, 6:38 p.m.
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Description Usage Arguments Details Value Slots See Also Examples
View source: R/initialize_peakPantheRAnnotation.R
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
Arguments
spectraPaths |
NULL or a character vector of spectra file paths, to set samples to process |
targetFeatTable |
NULL or a |
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: |
FIR |
A data.frame of Fallback Integration Regions (FIR) with
compounds as row and FIR parameters as columns: |
uROI |
A data.frame of updated Regions Of Interest (uROI) with
compounds as row and uROI parameters as columns: |
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 |
peakFit |
A list of length number of spectra files. Each list element is
a curveFit list of |
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
cpdIDA character vector of compound IDs, of length number of compounds
cpdNameA character vector of compound names, of length number of compounds
ROIA 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).FIRA 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).uROIA 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).filepathA character vector of file paths, of length number of spectra files
cpdMetadataA data.frame of compound metadata, with compounds as row and metadata as columns
spectraMetadataA data.frame of sample metadata, with samples as row and metadata as columns
acquisitionTimeA character vector of acquisition date-time (converted from POSIXct) or NA
uROIExistA logical stating if uROI have been set
useUROIA logical stating if uROI are to be used
useFIRA logical stating if FIR are to be used
TICA numeric vector of TIC or NA, of length number of spectra files
peakTablesA 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.
dataPointsA list of length number of spectra files. Each list element is a ROIsDataPoint list of
data.frameof raw data points for each ROI/uROI (retention time 'rt', mass 'mz' and intensity 'int' (as column) of each raw data points (as row))peakFitA list of length number of spectra files. Each list element is a curveFit list of
peakPantheR_curveFitor NA for each ROIisAnnotatedA logical stating if the annotation has taken place
Details:
The peakTables
data.frameare 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
See Also
Other peakPantheR:
peakPantheR_parallelAnnotation(),
peakPantheR_singleFileSearch()
Other parallelAnnotation:
peakPantheR_parallelAnnotation(),
peakPantheR_singleFileSearch()
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 | 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
}
|
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