MS backend accessing the MassBank MySQL database
Source:R/MsBackendMassbankSql-functions.R, R/MsBackendMassbankSql.R
MsBackendMassbankSql.RdThe MsBackendMassbankSql provides access to mass spectrometry data from
MassBank by directly accessing its
MySQL/MariaDb database. In addition it supports adding new spectra variables
or locally changing spectra variables provided by MassBank (without
changing the original values in the database).
Note that MsBackendMassbankSql requires a local installation of the
MassBank database since direct database access is not supported for the
main MassBank instance.
Also, some of the fields in the MassBank database are not directly compatible
with Spectra, such as the collision energy which is not available as a
numeric value. The collision energy as available in MassBank is reported as
spectra variable "collision_energy_text". Also, precursor m/z values
reported for some spectra can not be converted to a numeric and hence NA
is reported with the spectra variable precursorMz for these spectra. The
variable "precursor_mz_text" can be used to get the original precursor
m/z reported in MassBank.
Finally, MsBackendMassbankSql does not support parallel processing
because the database connection stored within the object can not be
shared acrcoss parallel processes. All functions on Spectra objects
with a MsBackendMassbankSql will (silently) disable parallel processing
even if the user provides a dedicated parallel processing setup with
the BPPARAM parameter.
Usage
MsBackendMassbankSql()
# S4 method for class 'MsBackendMassbankSql'
backendInitialize(object, dbcon, ...)
# S4 method for class 'MsBackendMassbankSql'
peaksData(object, columns = peaksVariables(object))
# S4 method for class 'MsBackendMassbankSql'
dataStorage(object)
# S4 method for class 'MsBackendMassbankSql'
intensity(object) <- value
# S4 method for class 'MsBackendMassbankSql'
mz(object) <- value
# S4 method for class 'MsBackendMassbankSql'
reset(object)
# S4 method for class 'MsBackendMassbankSql'
spectraData(object, columns = spectraVariables(object))
# S4 method for class 'MsBackendMassbankSql'
spectraNames(object)
# S4 method for class 'MsBackendMassbankSql'
spectraNames(object) <- value
# S4 method for class 'MsBackendMassbankSql'
tic(object, initial = TRUE)
# S4 method for class 'MsBackendMassbankSql'
x[i, j, ..., drop = FALSE]
# S4 method for class 'MsBackendMassbankSql,ANY'
extractByIndex(object, i)
# S4 method for class 'Spectra'
compounds(object, ...)
# S4 method for class 'MsBackendMassbankSql'
compounds(object, ...)
# S4 method for class 'MsBackendMassbankSql'
x$name <- value
# S4 method for class 'MsBackendMassbankSql'
precScanNum(object)
# S4 method for class 'MsBackendMassbankSql'
backendBpparam(object, BPPARAM = bpparam())Arguments
- object
Object extending
MsBackendMassbankSql.- dbcon
For
backendInitialize,MsBackendMassbankSql: SQL database connection to the MassBank (MariaDb) database.- ...
Additional arguments.
- columns
For
spectraDataaccessor: optionalcharacterwith column names (spectra variables) that should be included in the returnedDataFrame. By default, all columns are returned. ForpeaksDataaccessor: optionalcharacterwith requested columns in the individualmatrixof the returnedlist. UsepeaksVariables(object)for supported columns.- value
replacement value for
<-methods. See individual method description or expected data type.- initial
For
tic:logical(1)whether the initially reported total ion current should be reported, or whether the total ion current should be (re)calculated on the actual data (initial = FALSE).- x
Object extending
MsBackendMassbankSql.- i
For
[:integer,logicalorcharacterto subset the object.- j
For
[: not supported.- drop
For
[: not considered.- name
name of the variable to replace for
<-methods. See individual method description or expected data type.- BPPARAM
for
backendBpparam:BiocParallelparallel processing setup. Seebpparam()for more information.- spectraVariables
For
selectSpectraVariables:characterwith the names of the spectra variables to which the backend should be subsetted.
Supported Backend functions
The following functions are supported by the MsBackendMassbankSql.
[: subset the backend. Only subsetting by element (row/i) is allowed$,$<-: access or set/add a single spectrum variable (column) in the backend.acquisitionNum: returns the acquisition number of each spectrum. Returns anintegerof length equal to the number of spectra (withNA_integer_if not available).peaksDatareturns alistwith the spectras' peak data. The length of the list is equal to the number of spectra inobject. Each element of the list is amatrixwith columns"mz"and"intensity". For an empty spectrum, amatrixwith 0 rows and two columns (namedmzandintensity) is returned. Parametercolumnsallows to select which peaks variables to return, but supports currently only"mz"and"intensity".backendBpparam: whether the backend supports parallel processing. Takes aMsBackendMassbankSqland a parallel processing setup (seebpparam()for details) as input and always returns aSerialParam(). This function can be used to test whether a provided parallel processing setup is supported by the backend and returns the supported setup.backendInitialize: initialises the backend by retrieving the IDs of all spectra in the database. Parameterdbconwith the connection to the MassBank MySQL database is required.dataOrigin: gets acharacterof length equal to the number of spectra inobjectwith the data origin of each spectrum. This could e.g. be the mzML file from which the data was read.dataStorage: returns"<MassBank>"for all spectra.centroided,centroided<-: gets or sets the centroiding information of the spectra.centroidedreturns alogicalvector of length equal to the number of spectra withTRUEif a spectrum is centroided,FALSEif it is in profile mode andNAif it is undefined. See alsoisCentroidedfor estimating from the spectrum data whether the spectrum is centroided.valueforcentroided<-is either a singlelogicalor alogicalof length equal to the number of spectra inobject.collisionEnergy,collisionEnergy<-: gets or sets the collision energy for all spectra inobject.collisionEnergyreturns anumericwith length equal to the number of spectra (NA_real_if not present/defined),collisionEnergy<-takes anumericof length equal to the number of spectra inobject. Note that the collision energy description from MassBank are provided as spectra variable"collisionEnergyText".intensity: gets the intensity values from the spectra. Returns aNumericList()ofnumericvectors (intensity values for each spectrum). The length of thelistis equal to the number ofspectrainobject.ionCount: returns anumericwith the sum of intensities for each spectrum. If the spectrum is empty (seeisEmpty),NA_real_is returned.isCentroided: a heuristic approach assessing if the spectra inobjectare in profile or centroided mode. The function takes theqtlth quantile top peaks, then calculates the difference between adjacent m/z value and returnsTRUEif the first quartile is greater thank. (SeeSpectra:::.isCentroidedfor the code.)isEmpty: checks whether a spectrum inobjectis empty (i.e. does not contain any peaks). Returns alogicalvector of length equal number of spectra.isolationWindowLowerMz,isolationWindowLowerMz<-: gets or sets the lower m/z boundary of the isolation window.isolationWindowTargetMz,isolationWindowTargetMz<-: gets or sets the target m/z of the isolation window.isolationWindowUpperMz,isolationWindowUpperMz<-: gets or sets the upper m/z boundary of the isolation window.isReadOnly: returns alogical(1)whether the backend is read only or does allow also to write/update data.length: returns the number of spectra in the object.lengths: gets the number of peaks (m/z-intensity values) per spectrum. Returns anintegervector (length equal to the number of spectra). For empty spectra,0is returned.msLevel: gets the spectra's MS level. Returns anintegervector (of length equal to the number of spectra) with the MS level for each spectrum (orNA_integer_if not available).mz: gets the mass-to-charge ratios (m/z) from the spectra. Returns aNumericList()or length equal to the number of spectra, each element anumericvector with the m/z values of one spectrum.polarity,polarity<-: gets or sets the polarity for each spectrum.polarityreturns anintegervector (length equal to the number of spectra), with0and1representing negative and positive polarities, respectively.polarity<-expects an integer vector of length 1 or equal to the number of spectra.precursorCharge,precursorIntensity,precursorMz,precScanNum,precAcquisitionNum: get the charge (integer), intensity (numeric), m/z (numeric), scan index (integer) and acquisition number (interger) of the precursor for MS level 2 and above spectra from the object. Returns a vector of length equal to the number of spectra inobject.NAare reported for MS1 spectra of if no precursor information is available.reset: restores the backend to its original state, i.e. deletes all locally modified data and reinitializes the backend to the full data available in the database.rtime,rtime<-: gets or sets the retention times for each spectrum (in seconds).rtimereturns anumericvector (length equal to the number of spectra) with the retention time for each spectrum.rtime<-expects a numeric vector with length equal to the number of spectra.scanIndex: returns anintegervector with the scan index for each spectrum. This represents the relative index of the spectrum within each file. Note that this can be different to theacquisitionNumof the spectrum which is the index of the spectrum as reported in the mzML file.selectSpectraVariables: reduces the information within the backend to the selected spectra variables.smoothed,smoothed<-: gets or sets whether a spectrum is smoothed.smoothedreturns alogicalvector of length equal to the number of spectra.smoothed<-takes alogicalvector of length 1 or equal to the number of spectra inobject.spectraData: gets general spectrum metadata (annotation, also called header).spectraDatareturns aDataFrame. Note that replacing the spectra data withspectraData<-is not supported.spectraNames: returns acharactervector with the names of the spectra inobject.spectraVariables: returns acharactervector with the available spectra variables (columns, fields or attributes) available inobject. This should return all spectra variables which are present inobject, also"mz"and"intensity"(which are by default not returned by thespectraVariables,Spectramethod).tic: gets the total ion current/count (sum of signal of a spectrum) for all spectra inobject. By default, the value reported in the original raw data file is returned. For an empty spectrum,NA_real_is returned.
Not supported Backend functions
The following functions are not supported by the MsBackendMassbankSql since
the original data can not be changed.
backendMerge, export, filterDataStorage, filterPrecursorScan,
peaksData<-, filterAcquisitionNum, intensity<-, mz<-, precScanNum,
spectraData<-, spectraNames<-.
Retrieving compound annotations for spectra
While compound annotations are also provided via the spectraVariables of
the backend, it would also be possible to use the compounds function on
a Spectra object (that uses a MsBackendMassbankSql backend) to retrieve
compound annotations for the specific spectra.
Examples
## Create a connection to a database with MassBank data - in the present
## example we connect to a tiny SQLite database bundled in this package
## as public access to the MassBank MySQL is not (yet) supported. See the
## vignette for more information on how to install MassBank locally and
## enable MySQL database connections
library(RSQLite)
con <- dbConnect(SQLite(), system.file("sql", "minimassbank.sqlite",
package = "MsBackendMassbank"))
## Given that we have the connection to a MassBank databas we can
## initialize the backend:
be <- backendInitialize(MsBackendMassbankSql(), dbcon = con)
be
#> MsBackendMassbankSql with 70 spectra
#> msLevel precursorMz polarity
#> <integer> <numeric> <integer>
#> 1 2 506 0
#> 2 NA NA 1
#> 3 NA NA 0
#> 4 NA NA 1
#> 5 NA NA 0
#> ... ... ... ...
#> 66 2 185.028 0
#> 67 2 455.290 1
#> 68 2 253.051 0
#> 69 2 358.238 1
#> 70 2 256.170 1
#> ... 42 more variables/columns.
#> Use 'spectraVariables' to list all of them.
## Access MS level
msLevel(be)
#> [1] 2 NA NA NA NA 2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA 2 2 2 2 2
#> [26] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
#> [51] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
be$msLevel
#> [1] 2 NA NA NA NA 2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA 2 2 2 2 2
#> [26] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
#> [51] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
## Access m/z values
be$mz
#> NumericList of length 70
#> [[1]] 146.760803 158.863541 174.988785 ... 470.057434 487.989319 585.88446
#> [[2]] 22.99 23.07 23.19 38.98 53.15 60.08 ... 391.18 413.22 414.22 429.16 495.2
#> [[3]] 108.099566 152.005378 153.01824 ... 341.031964 409.06729 499.103447
#> [[4]] 137.0227 138.025605 139.034602 ... 304.271886 316.303106 352.234228
#> [[5]] 112.977759 205.053323 208.041128 ... 449.137152 671.1778 673.200866
#> [[6]] 78.893929 183.011719 193.957916 ... 328.091949 408.010193 426.021942
#> [[7]] 167.03389 168.040758 333.079965 ... 357.073039 365.040698 373.073473
#> [[8]] 195.09167 196.095033
#> [[9]] 108.096149 152.004656 153.01824 ... 359.997563 409.065314 491.043775
#> [[10]] 1278.12 1279.11 1279.18 1306.21 ... 2064.29 2091.32 2092.3 2136.33
#> ...
#> <60 more elements>
## Access the full spectra data (including m/z and intensity values)
spectraData(be)
#> DataFrame with 70 rows and 45 columns
#> msLevel rtime acquisitionNum scanIndex mz
#> <integer> <numeric> <integer> <integer> <NumericList>
#> 1 2 NA NA NA 146.761,158.864,174.989,...
#> 2 NA NA NA NA 22.99,23.07,23.19,...
#> 3 NA NA NA NA 108.100,152.005,153.018,...
#> 4 NA NA NA NA 137.023,138.026,139.035,...
#> 5 NA NA NA NA 112.978,205.053,208.041,...
#> ... ... ... ... ... ...
#> 66 2 NA NA NA 185.028
#> 67 2 NA NA NA 58.0653,77.0386,79.0543,...
#> 68 2 NA NA NA 132.021,133.029,135.009,...
#> 69 2 NA NA NA 53.0388,54.0340,55.0544,...
#> 70 2 NA NA NA 88.0757,151.0540,152.0620,...
#> intensity dataStorage dataOrigin centroided
#> <NumericList> <character> <character> <logical>
#> 1 0.980184,938.145447, 56.718353,... <MassBank> NA NA
#> 2 3173,2266, 880,... <MassBank> NA NA
#> 3 2809,119550, 91935,... <MassBank> NA NA
#> 4 157703, 23566, 5190,... <MassBank> NA NA
#> 5 5686, 927, 756,... <MassBank> NA NA
#> ... ... ... ... ...
#> 66 34967548 <MassBank> NA NA
#> 67 9143284, 341391,5278218,... <MassBank> NA NA
#> 68 82825.8,290504.6,301494.3,... <MassBank> NA NA
#> 69 1568742,19224644, 4676170,... <MassBank> NA NA
#> 70 678846, 403851,11111366,... <MassBank> NA NA
#> smoothed polarity precScanNum precursorMz precursorIntensity
#> <logical> <integer> <integer> <numeric> <numeric>
#> 1 NA 0 NA 506 408
#> 2 NA 1 NA NA NA
#> 3 NA 0 NA NA NA
#> 4 NA 1 NA NA NA
#> 5 NA 0 NA NA NA
#> ... ... ... ... ... ...
#> 66 NA 0 NA 185.028 185.028
#> 67 NA 1 NA 455.290 455.290
#> 68 NA 0 NA 253.051 253.051
#> 69 NA 1 NA 358.238 358.237
#> 70 NA 1 NA 256.170 256.169
#> precursorCharge collisionEnergy isolationWindowLowerMz
#> <integer> <numeric> <numeric>
#> 1 NA NA NA
#> 2 NA NA NA
#> 3 NA NA NA
#> 4 NA NA NA
#> 5 NA NA NA
#> ... ... ... ...
#> 66 NA NA NA
#> 67 NA NA NA
#> 68 NA NA NA
#> 69 NA NA NA
#> 70 NA NA NA
#> isolationWindowTargetMz isolationWindowUpperMz spectrum_id
#> <numeric> <numeric> <character>
#> 1 NA NA MCH00020
#> 2 NA NA MCH00002
#> 3 NA NA MCH00006
#> 4 NA NA MCH00009
#> 5 NA NA MCH00014
#> ... ... ... ...
#> 66 NA NA SM834451
#> 67 NA NA SM855703
#> 68 NA NA SM882851
#> 69 NA NA SM849703
#> 70 NA NA SM858801
#> spectrum_name date authors
#> <character> <character> <character>
#> 1 Adenosine 5'-triphos.. 2016.01.19 (Created .. Yoshikuni K, Tajiri ..
#> 2 Gentisic acid; MALDI.. 2016.01.19 (Created .. Wada Y, Osaka Medica..
#> 3 Gentisic acid; MALDI.. 2016.01.19 (Created .. Wada Y, Osaka Medica..
#> 4 5-Methoxysalicylic a.. 2016.01.19 (Created .. Wada Y, Osaka Medica..
#> 5 Sinapic acid; MALDI-.. 2016.01.19 (Created .. Wada Y, Osaka Medica..
#> ... ... ... ...
#> 66 m-Xylene-4-sulfonic .. 2016.12.12 Krauss M, Schymanski..
#> 67 Verapamil; LC-ESI-QF.. 2016.12.12 Krauss M, Schymanski..
#> 68 Daidzein; LC-ESI-QFT.. 2016.12.12 Krauss M, Schymanski..
#> 69 Oxybutynin; LC-ESI-Q.. 2016.12.12 Krauss M, Schymanski..
#> 70 Diphenhydramine; LC-.. 2019.11.20 (Created .. Krauss M, Schymanski..
#> license copyright publication
#> <character> <character> <character>
#> 1 CC BY-SA NA NA
#> 2 CC BY-SA NA NA
#> 3 CC BY-SA NA NA
#> 4 CC BY-SA NA NA
#> 5 CC BY-SA NA NA
#> ... ... ... ...
#> 66 CC BY Copyright (C) 2016 U.. Schymanski, E. L.; R..
#> 67 CC BY Copyright (C) 2016 U.. Schymanski, E. L.; R..
#> 68 CC BY Copyright (C) 2016 U.. Schymanski, E. L.; R..
#> 69 CC BY Copyright (C) 2016 U.. Schymanski, E. L.; R..
#> 70 CC BY Copyright (C) 2016 U.. Schymanski, E. L.; R..
#> splash compound_id adduct ionization
#> <character> <integer> <character> <character>
#> 1 splash10-0a4i-000090.. 1 [M-H]- NA
#> 2 splash10-004r-191300.. 2 NA NA
#> 3 splash10-0udi-090200.. 3 NA NA
#> 4 splash10-0fri-093000.. 4 NA NA
#> 5 splash10-006t-019080.. 5 NA NA
#> ... ... ... ... ...
#> 66 splash10-000i-090000.. 66 [M-H]- ESI
#> 67 splash10-066r-090030.. 67 [M+H]+ ESI
#> 68 splash10-0udi-009000.. 68 [M-H]- ESI
#> 69 splash10-0a4i-860900.. 69 [M+H]+ ESI
#> 70 splash10-014i-090000.. 70 [M+H]+ ESI
#> ionization_voltage fragmentation_mode collision_energy_text
#> <character> <character> <character>
#> 1 NA NA NA
#> 2 NA NA NA
#> 3 NA NA NA
#> 4 NA NA NA
#> 5 NA NA NA
#> ... ... ... ...
#> 66 NA HCD 35 (nominal)
#> 67 NA HCD 35 (nominal)
#> 68 NA HCD 35 (nominal)
#> 69 NA HCD 35 (nominal)
#> 70 NA HCD 35 (nominal)
#> instrument instrument_type formula exactmass
#> <character> <character> <character> <numeric>
#> 1 LTQ Orbitrap XL, The.. LC-ESI-ITFT C10H16N5O13P3 506.996
#> 2 Voyager DE-PRO, Appl.. MALDI-TOF C7H6O4 154.027
#> 3 Voyager DE-PRO, Appl.. MALDI-TOF C7H6O4 154.027
#> 4 Voyager DE-PRO, Appl.. MALDI-TOF C8H8O4 168.042
#> 5 Voyager DE-PRO, Appl.. MALDI-TOF C11H12O5 224.068
#> ... ... ... ... ...
#> 66 Q Exactive Plus Orbi.. LC-ESI-QFT C8H10O3S 186.035
#> 67 Q Exactive Plus Orbi.. LC-ESI-QFT C27H38N2O4 454.283
#> 68 Q Exactive Plus Orbi.. LC-ESI-QFT C15H10O4 254.058
#> 69 Q Exactive Plus Orbi.. LC-ESI-QFT C22H31NO3 357.230
#> 70 Q Exactive Plus Orbi.. LC-ESI-QFT C17H21NO 255.162
#> smiles inchi inchikey
#> <character> <character> <character>
#> 1 Nc(n3)c(n2)c(nc3)n(c.. InChI=1S/C10H16N5O13.. ZKHQWZAMYRWXGA-KQYNX..
#> 2 Oc(c1)cc(C(O)=O)c(O)c1 InChI=1S/C7H6O4/c8-4.. WXTMDXOMEHJXQO-UHFFF..
#> 3 Oc(c1)cc(C(O)=O)c(O)c1 InChI=1S/C7H6O4/c8-4.. WXTMDXOMEHJXQO-UHFFF..
#> 4 COc(c1)cc(C(O)=O)c(O.. InChI=1S/C8H8O4/c1-1.. IZZIWIAOVZOBLF-UHFFF..
#> 5 COC1=CC(=CC(=C1O)OC).. InChI=1S/C11H12O5/c1.. PCMORTLOPMLEFB-ONEGZ..
#> ... ... ... ...
#> 66 Cc1ccc(c(c1)C)S(=O)(.. InChI=1S/C8H10O3S/c1.. CHZLVSBMXZSPNN-UHFFF..
#> 67 COc1ccc(CCN(C)CCCC(C.. InChI=1S/C27H38N2O4/.. SGTNSNPWRIOYBX-UHFFF..
#> 68 OC1=CC=C(C=C1)C1=COC.. InChI=1S/C15H10O4/c1.. ZQSIJRDFPHDXIC-UHFFF..
#> 69 CCN(CC)CC#CCOC(=O)C(.. InChI=1S/C22H31NO3/c.. XIQVNETUBQGFHX-UHFFF..
#> 70 CN(C)CCOC(c1ccccc1)c.. InChI=1S/C17H21NO/c1.. ZZVUWRFHKOJYTH-UHFFF..
#> cas pubchem
#> <character> <character>
#> 1 56-65-5 CID:5957
#> 2 NA CID:3469
#> 3 NA CID:3469
#> 4 NA CID:75787
#> 5 530-59-6 CID:637775
#> ... ... ...
#> 66 88-61-9 CID:6938
#> 67 52-53-9 CID:2520
#> 68 486-66-8 CID:5281708
#> 69 5633-20-5 CID:4634
#> 70 58-73-1 CID:3100
#> synonym
#> <CharacterList>
#> 1 Adenosine 5'-triphos..,ATP
#> 2 2,5-Dihydroxybenzoic..,Gentisic acid
#> 3 2,5-Dihydroxybenzoic..,DHB,Gentisic acid
#> 4 5-Methoxysalicylic a..,DHBs (Super DHB)
#> 5 Sinapic acid,3,5-dimethoxy-4-hydr..,3-(4-hydroxy-3,5-dim..
#> ... ...
#> 66 m-Xylene-4-sulfonic ..,2,4-dimethylbenzenes..
#> 67 Verapamil,2-(3,4-dimethoxyphen..
#> 68 Daidzein,7-hydroxy-3-(4-hydro..
#> 69 Oxybutynin,4-(diethylamino)but-..
#> 70 Diphenhydramine,2-benzhydryloxy-N,N-..
#> precursor_mz_text compound_name
#> <character> <character>
#> 1 506.000000 Adenosine 5'-triphos..
#> 2 NA 2,5-Dihydroxybenzoic..
#> 3 NA 2,5-Dihydroxybenzoic..
#> 4 NA 5-Methoxysalicylic a..
#> 5 NA Sinapic acid
#> ... ... ...
#> 66 185.0278 m-Xylene-4-sulfonic ..
#> 67 455.2904 Verapamil
#> 68 253.0506 Daidzein
#> 69 358.2377 Oxybutynin
#> 70 256.1696 Diphenhydramine
## Add a new spectra variable
be$new_variable <- "b"
be$new_variable
#> [1] "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b"
#> [20] "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b"
#> [39] "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b"
#> [58] "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b"
## Subset the backend
be_sub <- be[c(3, 1)]
spectraNames(be)
#> [1] "MCH00020" "MCH00002" "MCH00006" "MCH00009" "MCH00014" "MCH00019"
#> [7] "MCH00012" "MCH00003" "MCH00016" "MCH00001" "MCH00018" "MCH00007"
#> [13] "MCH00013" "MCH00015" "MCH00008" "MCH00004" "MCH00005" "MCH00011"
#> [19] "MCH00017" "MCH00010" "SM864952" "SM823851" "SM868004" "SM862204"
#> [25] "SM834302" "SM810352" "SM847101" "SM861203" "SM839603" "SM829401"
#> [31] "SM814501" "SM858902" "SM850104" "SM854403" "SM836003" "SM821703"
#> [37] "SM880602" "SM868101" "SM851552" "SM804503" "SM848503" "SM842251"
#> [43] "SM817703" "SM847302" "SM805801" "SM820101" "SM816753" "SM805001"
#> [49] "SM838051" "SM812904" "SM840401" "SM812701" "SM861901" "SM874401"
#> [55] "SM838502" "SM857001" "SM858203" "SM847702" "SM883903" "SM818403"
#> [61] "SM871101" "SM842156" "SM841901" "SM854306" "SM878551" "SM834451"
#> [67] "SM855703" "SM882851" "SM849703" "SM858801"
spectraNames(be_sub)
#> [1] "MCH00006" "MCH00020"