MsBackend representing MS data from MetaboLights
Source:R/MsBackendMetaboLights.R
MsBackendMetaboLights.RdMsBackendMetaboLights retrieves and represents mass spectrometry (MS)
data from metabolomics experiments stored in the
MetaboLights repository. The backend
directly extends the MsBackendMzR backend from the Spectra package and
hence supports MS data in mzML, netCDF and mzXML format. Data in other
formats can not be loaded with MsBackendMetaboLights. Upon initialization
with the backendInitialize() method, the MsBackendMetaboLights backend
downloads and caches the MS data files of an experiment locally avoiding
hence repeated download of the data.
Arguments
- object
an instance of
MsBackendMetaboLights.- mtblsId
character(1)with the ID of a single MetaboLights data set/experiment.- assayName
characterwith the file names of assay files of the data set. If not provided (assayName = character(), the default), MS data files of all data set's assays are loaded. Usemtbls_list_files(<MetaboLights ID>, pattern = "^a_")to list all available assay files of a data set<MetaboLights ID>.- filePattern
characterwith the pattern defining the supported (or requested) file types. Defaults tofilePattern = "mzML$|CDF$|cdf$|mzXML$"hence restricting to mzML, CDF and mzXML files which are supported by Spectra'sMsBackendMzRbackend.- offline
logical(1)whether only locally cached content should be evaluated/loaded.- ...
additional parameters; currently ignored.
Value
For
MsBackendMetaboLights(): an instance ofMsBackendMetaboLights.For
backendInitialize(): an instance ofMsBackendMetaboLightswith the MS data of the specified MetaboLights data set.
Details
File names for data files are by default extracted from the column
"Derived Spectral Data File" of the MetaboLights data set's assay
table. If this column does not contain any supported file names, the
assay's column "Raw Spectral Data File" is evaluated instead.
The backend uses the BiocFileCache package for caching of the data files. These are stored in the default local BiocFileCache cache along with additional metadata that includes the MetaboLights ID and the assay file name with which the data file is associated with. Note that at present only MS data files in mzML, CDF and mzXML format are supported.
The MsBackendMetaboLights backend defines and provides additional spectra
variables "mtbls_id", "mtbls_assay_name" and
"derived_spectral_data_file" that list the MetaboLights ID, the name of
the assay file and the original data file name on the MetaboLights ftp
server for each individual spectrum. The "derived_spectral_data_file" can
be used for the mapping between the experiment's samples and the
individual data files, respective their spectra. This mapping is provided
in the MetaboLights assay file.
The MsBackendMetaboLights backend is considered read-only and does
thus not support changing m/z and intensity values directly.
Also, merging of MS data of MsBackendMetaboLights is not supported and
thus c() of several Spectra with MS data represented by
MsBackendMetaboLights will throw an error.
Initialization and loading of data
New instances of the class can be created with the MsBackendMetaboLights()
function. Data is loaded and initialized using the backendInitialize()
function which can be configured with parameters mtblsId, assayName and
filePattern. mtblsId must be the ID of a single (existing)
MetaboLights data set. Parameter assayName allows to define specific
assays of the MetaboLights data set from which the data files should be
loaded. If provided, it should be the file name(s) of the respective
assay(s) in MetaboLights (use e.g.
mtbls_list_files(<MetaboLights ID>, pattern = "^a_") to list all available
assay files for a given MetaboLights ID <MetaboLights ID>). By default,
with assayName = character() MS data files from all assays of a data
set are loaded. Optional parameter filePattern defines the pattern that
should be used to filter the file names of the MS data files. It defaults
to data files with file endings of supported MS data files.
backendInitialize() requires an active internet connection as the
function first compares the remote file content to the locally cached files
and eventually synchronizes changes/updates. This can be skipped with
offline = TRUE in which case only locally cached content is queried.
Examples
library(MsBackendMetaboLights)
## List files of a MetaboLights data set
mtbls_list_files("MTBLS39")
#> [1] "FILES"
#> [2] "a_MTBLS39_the_plasticity_of_the_grapevine_berry_transcriptome_metabolite_profiling_mass_spectrometry.txt"
#> [3] "i_Investigation.txt"
#> [4] "m_MTBLS39_the_plasticity_of_the_grapevine_berry_transcriptome_metabolite_profiling_mass_spectrometry_v2_maf.tsv"
#> [5] "metexplore_mapping.json"
#> [6] "s_MTBLS39.txt"
## Initialize a MsBackendMetaboLights representing all MS data files of
## the data set with the ID "MTBLS39". This will download and cache all
## files and subsequently load and represent them in R.
be <- backendInitialize(MsBackendMetaboLights(), "MTBLS39")
#> Used data files from the assay's column "Raw Spectral Data File" since none were available in column "Derived Spectral Data File".
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN063B.cdf'
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN063C.cdf'
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS063B.cdf'
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS063C.cdf'
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM063B.cdf'
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM063C.cdf'
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073A.cdf'
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073B.cdf'
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073C.cdf'
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073A.cdf'
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073B.cdf'
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073C.cdf'
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073A.cdf'
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073B.cdf'
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073C.cdf'
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083A.cdf'
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083B.cdf'
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083C.cdf'
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083A.cdf'
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083B.cdf'
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083C.cdf'
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083A.cdf'
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083B.cdf'
#> adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083C.cdf'
be
#> MsBackendMetaboLights with 15141 spectra
#> msLevel rtime scanIndex
#> <integer> <numeric> <integer>
#> 1 1 0.296384 1
#> 2 1 6.206912 2
#> 3 1 12.093056 3
#> 4 1 17.942912 4
#> 5 1 23.835072 5
#> ... ... ... ...
#> 15137 1 2682.81 596
#> 15138 1 2687.29 597
#> 15139 1 2691.77 598
#> 15140 1 2696.27 599
#> 15141 1 2700.81 600
#> ... 36 more variables/columns.
#>
#> file(s):
#> MN063A.cdf
#> CS063A.cdf
#> AM063A.cdf
#> ... 24 more files