peakPantheR_singleFileSearch: Search, integrate and report targeted features in a raw...
In peakPantheR: Peak Picking and Annotation of High Resolution Experiments
Description
Usage
Arguments
Value
See Also
Examples
View source: R/peakPantheR_singleFileSearch.R
Description
Report for a raw spectra the TIC, acquisition time, integrated
targeted features, fitted curves and datapoints for each region of interest.
Optimised to reduce the number of file access. Features not detected can be
integrated using fallback integration regions (FIR).
Usage
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Arguments
singleSpectraDataPath
(str) path to netCDF or mzML raw data file
(centroided, only with the channel of interest).
targetFeatTable
a data.frame of compounds to target as
rows. 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).
peakStatistic
(bool) If TRUE calculates additional peak statistics:
'ppm_error', 'rt_dev_sec', 'tailing factor' and 'asymmetry factor'
plotEICsPath
(str or NA) If not NA, will save a .png of all ROI
EICs at the path provided ('filepath/filename.png' expected). If NA no
plot saved
getAcquTime
(bool) If TRUE will extract sample acquisition date-time
from the mzML metadata (the additional file access will impact run time)
FIR
(data.frame or NULL) If not NULL, integrate Fallback Integration
Regions (FIR) when a feature is not found. Compounds as row are identical to
targetFeatTable, columns are rtMin (float in seconds),
rtMax (float in seconds), mzMin (float), mzMax (float).
centroided
(bool) use TRUE if the data is centroided, used by
readMSData when reading the raw data file
curveModel
(str) specify the peak-shape model to fit,
by default skewedGaussian.
Accepted values are skewedGaussian and emgGaussian
verbose
(bool) If TRUE message calculation progress, time taken and
number of features found
...
Passes arguments to findTargetFeatures to alter
peak-picking parameters (e.g. curveModel, sampling,
params as a list of parameters for each ROI or 'guess',...)
Value
a list: list()$TIC (int) TIC value,
list()$peakTable (data.frame) targeted features results
(see Details), list()$curveFit (list) list of
peakPantheR_curveFit or NA for each ROI, list()$acquTime
(POSIXct or NA) date-time of sample acquisition from mzML metadata,
list()$ROIsDataPoint (list) a list of data.frame of raw
data points for each ROI (retention time 'rt', mass 'mz' and intensity 'int'
(as column) of each raw data points (as row)).
Details:
The returned peakTable data.frame is 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:
peakPantheRAnnotation,
peakPantheR_parallelAnnotation()
Other parallelAnnotation:
peakPantheRAnnotation,
peakPantheR_parallelAnnotation()
Examples
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if(requireNamespace('faahKO')){
## Load data
library(faahKO)
netcdfFilePath <- system.file('cdf/KO/ko15.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))
res <- peakPantheR_singleFileSearch(netcdfFilePath,targetFeatTable,
peakStatistic=TRUE)
# Polarity can not be extracted from netCDF files, please set manually the
# polarity with the 'polarity' method.
# Reading data from 2 windows
# Data read in: 0.16 secs
# Warning: rtMin/rtMax outside of ROI; datapoints cannot be used for
# mzMin/mzMax calculation, approximate mz and returning ROI$mzMin and
# ROI$mzMax for ROI #1
# Found 2/2 features in 0.05 secs
# Peak statistics done in: 0 secs
# Feature search done in: 0.75 secs
res
# $TIC
# [1] 2410533091
#
# $peakTable
# found rtMin rt rtMax mzMin mz mzMax peakArea
# 1 TRUE 3309.759 3346.828 3385.410 522.1948 522.2 522.2052 26133727
# 2 TRUE 3345.377 3386.529 3428.279 496.2000 496.2 496.2000 35472141
# maxIntMeasured maxIntPredicted cpdID cpdName is_filled ppm_error
# 1 889280 901015.8 ID-1 Cpd 1 FALSE 0.02337616
# 2 1128960 1113576.7 ID-2 Cpd 2 FALSE 0.02460103
# rt_dev_sec tailingFactor asymmetryFactor
# 1 1.9397590 1.015357 1.026824
# 2 0.9518072 1.005378 1.009318
#
# $acquTime
# [1] NA
#
#
# $curveFit
# $curveFit[[1]]
# $amplitude
# [1] 162404.8
#
# $center
# [1] 3341.888
#
# $sigma
# [1] 0.07878613
#
# $gamma
# [1] 0.00183361
#
# $fitStatus
# [1] 2
#
# $curveModel
# [1] 'skewedGaussian'
#
# attr(,'class')
# [1] 'peakPantheR_curveFit'
#
# $curveFit[[2]]
# $amplitude
# [1] 199249.1
#
# $center
# [1] 3382.577
#
# $sigma
# [1] 0.07490442
#
# $gamma
# [1] 0.00114719
#
# $fitStatus
# [1] 2
#
# $curveModel
# [1] 'skewedGaussian'
#
# attr(,'class')
# [1] 'peakPantheR_curveFit'
#
#
# $ROIsDataPoint
# $ROIsDataPoint[[1]]
# rt mz int
# 1 3315.154 522.2 2187
# 2 3316.719 522.2 3534
# 3 3318.284 522.2 6338
# 4 3319.849 522.2 11718
# 5 3321.414 522.2 21744
# 6 3322.979 522.2 37872
# 7 3324.544 522.2 62424
# 8 3326.109 522.2 98408
# 9 3327.673 522.2 152896
# 10 3329.238 522.2 225984
# ...
#
# $ROIsDataPoint[[2]]
# rt mz int
# 1 3280.725 496.2 1349
# 2 3290.115 496.2 2069
# 3 3291.680 496.2 3103
# 4 3293.245 496.2 5570
# 5 3294.809 496.2 10730
# 6 3296.374 496.2 20904
# 7 3297.939 496.2 38712
# 8 3299.504 496.2 64368
# 9 3301.069 496.2 97096
# 10 3302.634 496.2 136320
# ...
}
peakPantheR documentation built on Nov. 8, 2020, 6:38 p.m.
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Description Usage Arguments Value See Also Examples
View source: R/peakPantheR_singleFileSearch.R
Description
Report for a raw spectra the TIC, acquisition time, integrated targeted features, fitted curves and datapoints for each region of interest. Optimised to reduce the number of file access. Features not detected can be integrated using fallback integration regions (FIR).
Usage
1 2 3 4 5 6 7 8 9 10 11 12 |
Arguments
singleSpectraDataPath |
(str) path to netCDF or mzML raw data file (centroided, only with the channel of interest). |
targetFeatTable |
a |
peakStatistic |
(bool) If TRUE calculates additional peak statistics: 'ppm_error', 'rt_dev_sec', 'tailing factor' and 'asymmetry factor' |
plotEICsPath |
(str or NA) If not NA, will save a .png of all ROI
EICs at the path provided ( |
getAcquTime |
(bool) If TRUE will extract sample acquisition date-time from the mzML metadata (the additional file access will impact run time) |
FIR |
(data.frame or NULL) If not NULL, integrate Fallback Integration
Regions (FIR) when a feature is not found. Compounds as row are identical to
|
centroided |
(bool) use TRUE if the data is centroided, used by
|
curveModel |
(str) specify the peak-shape model to fit,
by default |
verbose |
(bool) If TRUE message calculation progress, time taken and number of features found |
... |
Passes arguments to |
Value
a list: list()$TIC (int) TIC value,
list()$peakTable (data.frame) targeted features results
(see Details), list()$curveFit (list) list of
peakPantheR_curveFit or NA for each ROI, list()$acquTime
(POSIXct or NA) date-time of sample acquisition from mzML metadata,
list()$ROIsDataPoint (list) a list of data.frame of raw
data points for each ROI (retention time 'rt', mass 'mz' and intensity 'int'
(as column) of each raw data points (as row)).
Details:
The returned peakTable data.frame is 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:
peakPantheRAnnotation,
peakPantheR_parallelAnnotation()
Other parallelAnnotation:
peakPantheRAnnotation,
peakPantheR_parallelAnnotation()
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 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 | if(requireNamespace('faahKO')){
## Load data
library(faahKO)
netcdfFilePath <- system.file('cdf/KO/ko15.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))
res <- peakPantheR_singleFileSearch(netcdfFilePath,targetFeatTable,
peakStatistic=TRUE)
# Polarity can not be extracted from netCDF files, please set manually the
# polarity with the 'polarity' method.
# Reading data from 2 windows
# Data read in: 0.16 secs
# Warning: rtMin/rtMax outside of ROI; datapoints cannot be used for
# mzMin/mzMax calculation, approximate mz and returning ROI$mzMin and
# ROI$mzMax for ROI #1
# Found 2/2 features in 0.05 secs
# Peak statistics done in: 0 secs
# Feature search done in: 0.75 secs
res
# $TIC
# [1] 2410533091
#
# $peakTable
# found rtMin rt rtMax mzMin mz mzMax peakArea
# 1 TRUE 3309.759 3346.828 3385.410 522.1948 522.2 522.2052 26133727
# 2 TRUE 3345.377 3386.529 3428.279 496.2000 496.2 496.2000 35472141
# maxIntMeasured maxIntPredicted cpdID cpdName is_filled ppm_error
# 1 889280 901015.8 ID-1 Cpd 1 FALSE 0.02337616
# 2 1128960 1113576.7 ID-2 Cpd 2 FALSE 0.02460103
# rt_dev_sec tailingFactor asymmetryFactor
# 1 1.9397590 1.015357 1.026824
# 2 0.9518072 1.005378 1.009318
#
# $acquTime
# [1] NA
#
#
# $curveFit
# $curveFit[[1]]
# $amplitude
# [1] 162404.8
#
# $center
# [1] 3341.888
#
# $sigma
# [1] 0.07878613
#
# $gamma
# [1] 0.00183361
#
# $fitStatus
# [1] 2
#
# $curveModel
# [1] 'skewedGaussian'
#
# attr(,'class')
# [1] 'peakPantheR_curveFit'
#
# $curveFit[[2]]
# $amplitude
# [1] 199249.1
#
# $center
# [1] 3382.577
#
# $sigma
# [1] 0.07490442
#
# $gamma
# [1] 0.00114719
#
# $fitStatus
# [1] 2
#
# $curveModel
# [1] 'skewedGaussian'
#
# attr(,'class')
# [1] 'peakPantheR_curveFit'
#
#
# $ROIsDataPoint
# $ROIsDataPoint[[1]]
# rt mz int
# 1 3315.154 522.2 2187
# 2 3316.719 522.2 3534
# 3 3318.284 522.2 6338
# 4 3319.849 522.2 11718
# 5 3321.414 522.2 21744
# 6 3322.979 522.2 37872
# 7 3324.544 522.2 62424
# 8 3326.109 522.2 98408
# 9 3327.673 522.2 152896
# 10 3329.238 522.2 225984
# ...
#
# $ROIsDataPoint[[2]]
# rt mz int
# 1 3280.725 496.2 1349
# 2 3290.115 496.2 2069
# 3 3291.680 496.2 3103
# 4 3293.245 496.2 5570
# 5 3294.809 496.2 10730
# 6 3296.374 496.2 20904
# 7 3297.939 496.2 38712
# 8 3299.504 496.2 64368
# 9 3301.069 496.2 97096
# 10 3302.634 496.2 136320
# ...
}
|
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