Store contents of MS objects as plain text files

The saveMsObject() and readMsObject() methods with the PlainTextParam option enable users to save/load different type of mass spectrometry (MS) object as a collections of plain text files in/from a specified folder. This folder, defined with the path parameter, will be created by the storeResults() function. Writing data to a folder that contains already exported data will result in an error.

All data is exported to plain text files, where possible as tabulator delimited text files. Data is exported using R's write.table() function, thus, the text files will also contain row names (first column) as well as column names (header). Strings in the text files are quoted. Some information, in particular the content of parameter classes within the objects, is stored in JSON format instead.

The MS object currently supported for import and export with this parameter are:

MsBackendMzR object, defined in the (Spectra) package.
Spectra object, defined in the (Spectra) package.
MsExperiment object, defined in the (MsExperiment) package.
XcmsExperiment object, defined in the (xcms) package.

See their respective section below for details and formats of the exported files.

Usage

PlainTextParam(path = tempdir())

# S4 method for class 'MsBackendMzR,PlainTextParam'
saveMsObject(object, param)

# S4 method for class 'MsBackendMzR,PlainTextParam'
readMsObject(object, param, spectraPath = character())

# S4 method for class 'MsExperiment,PlainTextParam'
saveMsObject(object, param)

# S4 method for class 'MsExperiment,PlainTextParam'
readMsObject(object, param, ...)

# S4 method for class 'Spectra,PlainTextParam'
saveMsObject(object, param)

# S4 method for class 'Spectra,PlainTextParam'
readMsObject(object, param, ...)

# S4 method for class 'XcmsExperiment,PlainTextParam'
saveMsObject(object, param)

# S4 method for class 'XcmsExperiment,PlainTextParam'
readMsObject(object, param, ...)

Arguments

path: For PlainTextParam(): character(1), defining where the files are going to be stored/ should be loaded from. The default is path = tempdir().
object: for saveMsObject(): the MS data object to save, for readMsObject(): the MS data object that should be returned
param: an object defining and (eventually configuring) the file format and file name or directory to/from which the data object should be exported/imported.
spectraPath: For readMsObject(): character(1) optionally allowing to define the (absolute) path where the spectra files (data storage files) can be found. This parameter is used for MsBackendMzR (see descriptions below) and can be passed through ... also to readMsObject() functions for other classes (such as Spectra, MsExperiment etc).
...: Additional parameters passed down to internal functions. E.g. parameter spectraPath (see above).

Value

For PlainTextParam(): a PlainTextParam class. saveMsObject() does not return anything but saves the object to collections of different plain text files to a folder. The readMsObject() method returns the restored data as an instance of the class specified with parameter object.

On-disk storage for `MsBackendMzR` objects

For MsBackendMzR objects, defined in the Spectra package, the following file is stored:

The backend's spectraData() is stored in a tabular format in a text file named ms_backend_data.txt. Each row of this tab-delimited text file corresponds to a spectrum with its respective metadata in the columns.

On-disk storage for `Spectra` objects

For Spectra objects, defined in the Spectra package, the files listed below are stored. Any parameter passed to the saveMsObject() method using its ... parameter are passed to the saveMsObject() call of the Spectra's backend.

The processingQueueVariables, processing, processingChunkSize(), and backend class information of the object are stored in a text file named spectra_slots.txt. Each of these slots is stored such that the name of the slot is written, followed by "=" and the content of the slot.
The processing queue of the Spectra object, ensuring that any spectra data modifications are retained, is stored in a json file named spectra_processing_queue.json. The file is written such that each processing step is separated by a line and includes all information about the parameters and functions used for the step.
The Spectra's MS data (i.e. it's backend) is stored/exported using the saveMsObject() method of the respective backend type. Currently only backends for which the saveMsObject() method is implemented (see above) are supported.

On-disk storage for `MsExperiment` objects

For MsExperiment objects, defined in the MsExperiment package, the exported data and related text files are listed below. Any parameter passed to the saveMsObject() through ... are passed to the saveMsObject() calls of the individual MS data object(s) within the MsExperiment.

Note that at present saveMsObject() with PlainTextParam does not export the full content of the MsExperiment, i.e. slots @experimentFiles, @qdata, @otherData and @metadata are currently not saved.

The sampleData() is stored as a text file named ms_experiment_sample_data.txt. Each row of this file corresponds to a sample with its respective metadata in the columns.
The links between the sample data and any other data within the MsExperiment are stored in text files named ms_experiment_sample_data_links_....txt, with "..." referring to the data slot to which samples are linked. Each file contains the mapping between the sample data and the elements in a specific data slot (e.g., Spectra). The files are tabulator delimited text files with two columns of integer values, the first representing the index of a sample in the objects sampleData(), the second the index of the assigned element in the respective object slot. The table "ms_experiment_element_metadata.txt" contains the metadata of each of the available mappings.
If the MsExperiment contains a Spectra object with MS data, it's content is exported to the same folder using a saveMsObject() call on it (see above for details of exporting Spectra objects to text files).

On-disk storage for `XcmsExperiment` objects

For XcmsExperiment objects, defined in the xcms package, the exported data and related text files are listed below. Any parameter passed to the saveMsObject() through ... are passed to the saveMsObject() calls of the individual MS data object(s) within the XcmsExperiment.

The chromatographic peak information obtained with chromPeaks() and chromPeaksData() is stored in tabular format in the text files xcms_experiment_chrom_peaks.txt and xcms_experiment_chrom_peak_data.txt, respectively. The first file's rows represent single peaks with their respective metadata in the columns (only numeric information). The second file contains arbitrary additional information/metadata for each peak (each row being one chrom peak).
The featureDefinitions() are stored in a text file named xcms_experiment_feature_definitions.txt. Additionally, a second file named ms_experiment_feature_peak_index.txt is generated to connect the features with the corresponding chromatographic peaks. Each row of the first file corresponds to a feature with its respective metadata in the columns. The second file contains the mapping between features and chromatographic peaks (one peak ID per row).
The processHistory() information of the object is stored to a file named xcms_experiment_process_history.json in JSON format.
The XcmsExperiment directly extends the MsExperiment class, thus, any MS data is saved using a call to the saveMsObject of the MsExperiment (see above for more information).

Author

Philippine Louail

Examples


## Export and import a `Spectra` object:

library(Spectra)
library(msdata)
fl <- system.file("TripleTOF-SWATH", "PestMix1_DDA.mzML", package = "msdata")
sps <- Spectra(fl)

## Export the object to a temporary directory
d <- file.path(tempdir(), "spectra_example")
saveMsObject(sps, PlainTextParam(d))

## List the exported plain text files:
dir(d)
#> [1] "OBJECT"                        "backend"                      
#> [3] "metadata"                      "ms_backend_data.txt"          
#> [5] "processing"                    "processing_chunk_size"        
#> [7] "processing_queue_variables"    "spectra_processing_queue.json"
#> [9] "spectra_slots.txt"            

## - ms_backend_data.txt contains the metadata for the MS backend used (a
##   'MsBackendMzR`.
## - spectra_slots.txt contains general information from the Spectra object.

## Import the data again. By using `Spectra()` as first parameter we ensure
## the result is returned as a `Spectra` object.
sps_in <- readMsObject(Spectra(), PlainTextParam(d))
#> backend MsBackendMzR
sps_in
#> MSn data (Spectra) with 7602 spectra in a MsBackendMzR backend:
#>        msLevel     rtime scanIndex
#>      <integer> <numeric> <integer>
#> 1            1     0.231         1
#> 2            1     0.351         2
#> 3            1     0.471         3
#> 4            1     0.591         4
#> 5            1     0.711         5
#> ...        ...       ...       ...
#> 7598         1   899.491      7598
#> 7599         1   899.613      7599
#> 7600         1   899.747      7600
#> 7601         1   899.872      7601
#> 7602         1   899.993      7602
#>  ... 27 more variables/columns.
#> 
#> file(s):
#> PestMix1_DDA.mzML

## Check that the data is the same
all.equal(rtime(sps), rtime(sps_in))
#> [1] TRUE
all.equal(intensity(sps), intensity(sps_in))
#> [1] TRUE

## The data got exported *by module*, thus we could also load only a part of
## the exported data, such as just the `MsBackend` used by the `Spectra`:
be <- readMsObject(MsBackendMzR(), PlainTextParam(d))
be
#> MsBackendMzR with 7602 spectra
#>        msLevel     rtime scanIndex
#>      <integer> <numeric> <integer>
#> 1            1     0.231         1
#> 2            1     0.351         2
#> 3            1     0.471         3
#> 4            1     0.591         4
#> 5            1     0.711         5
#> ...        ...       ...       ...
#> 7598         1   899.491      7598
#> 7599         1   899.613      7599
#> 7600         1   899.747      7600
#> 7601         1   899.872      7601
#> 7602         1   899.993      7602
#>  ... 27 more variables/columns.
#> 
#> file(s):
#> PestMix1_DDA.mzML

## The export functionality also ensures that the data/object can be
## completely restored, i.e., for `Spectra` objects also their
## *processing queue* is preserved/stored. To show this we below first
## filter the spectra object by retention time and m/z:

sps_filt <- sps |>
    filterRt(c(400, 600)) |>
    filterMzRange(c(200, 300))
## The filtered object has less spectra
length(sps_filt)
#> [1] 2054
length(sps)
#> [1] 7602
## And also less mass peaks per spectrum
lengths(sps_filt[1:3])
#> [1]   0   0 101
lengths(sps[1:3])
#> [1] 223 211 227

d <- file.path(tempdir(), "spectra_example2")
saveMsObject(sps_filt, PlainTextParam(d))

## The directory contains now an additional file with the processing
## queue of the `Spectra`.
dir(d)
#> [1] "ms_backend_data.txt"           "spectra_processing_queue.json"
#> [3] "spectra_slots.txt"            

## Restoring the object again.
sps_in <- readMsObject(Spectra(), PlainTextParam(d))
#> backend MsBackendMzR

## Both objects have the same processing history
sps_filt
#> MSn data (Spectra) with 2054 spectra in a MsBackendMzR backend:
#>        msLevel     rtime scanIndex
#>      <integer> <numeric> <integer>
#> 1            2   400.088      3242
#> 2            2   400.208      3243
#> 3            1   400.346      3244
#> 4            2   400.498      3245
#> 5            2   400.618      3246
#> ...        ...       ...       ...
#> 2050         2   599.253      5291
#> 2051         2   599.373      5292
#> 2052         1   599.511      5293
#> 2053         1   599.636      5294
#> 2054         2   599.904      5295
#>  ... 33 more variables/columns.
#> 
#> file(s):
#> PestMix1_DDA.mzML
#> Lazy evaluation queue: 1 processing step(s)
#> Processing:
#>  Filter: select retention time [400..600] on MS level(s) 1 2 [Thu Sep 19 13:35:49 2024]
#>  Filter: select peaks with an m/z within [200, 300] [Thu Sep 19 13:35:49 2024] 
sps_in
#> MSn data (Spectra) with 2054 spectra in a MsBackendMzR backend:
#>        msLevel     rtime scanIndex
#>      <integer> <numeric> <integer>
#> 1            2   400.088      3242
#> 2            2   400.208      3243
#> 3            1   400.346      3244
#> 4            2   400.498      3245
#> 5            2   400.618      3246
#> ...        ...       ...       ...
#> 2050         2   599.253      5291
#> 2051         2   599.373      5292
#> 2052         1   599.511      5293
#> 2053         1   599.636      5294
#> 2054         2   599.904      5295
#>  ... 27 more variables/columns.
#> 
#> file(s):
#> PestMix1_DDA.mzML
#> Lazy evaluation queue: 1 processing step(s)
#> Processing:
#>  Filter: select retention time [400..600] on MS level(s) 1 2 [Thu Sep 19 13:35:49 2024]
#>  Filter: select peaks with an m/z within [200, 300] [Thu Sep 19 13:35:49 2024] 

## Same number of spectra
length(sps_filt)
#> [1] 2054
length(sps_in)
#> [1] 2054

## Same number of mass peaks (after filtering)
lengths(sps_filt[1:3])
#> [1]   0   0 101
lengths(sps_in[1:3])
#> [1]   0   0 101

Store contents of MS objects as plain text files

Usage

Arguments

Value

On-disk storage for MsBackendMzR objects

On-disk storage for Spectra objects

On-disk storage for MsExperiment objects

On-disk storage for XcmsExperiment objects