XCMSnExp filtering and subsetting

The methods listed on this page allow to filter and subset XCMSnExp objects. Most of them are inherited from the OnDiskMSnExp object defined in the MSnbase package and have been adapted for XCMSnExp to enable correct subsetting of preprocessing results.

[: subset a XCMSnExp object by spectra. Be aware that this removes all preprocessing results, except adjusted retention times if keepAdjustedRtime = TRUE is passed to the method.
[[: extracts a single Spectrum object (defined in MSnbase). The reported retention time is the adjusted retention time if alignment has been performed.
filterChromPeaks: subset the chromPeaks matrix in object. Parameter method allows to specify how the chromatographic peaks should be filtered. Currently, only method = "keep" is supported which allows to specify chromatographic peaks to keep with parameter keep (i.e. provide a logical, integer or character defining which chromatographic peaks to keep). Feature definitions (if present) are updated correspondingly.
filterFeatureDefinitions: allows to subset the feature definitions of an XCMSnExp object. Parameter features allow to define which features to keep. It can be a logical, integer (index of features to keep) or character (feature IDs) vector.
filterFile: allows to reduce the XCMSnExp to data from only selected files. Identified chromatographic peaks for these files are retained while correspondence results (feature definitions) are removed by default. To force keeping feature definitions use keepFeatures = TRUE. Adjusted retention times (if present) are retained by default if present. Use keepAdjustedRtime = FALSE to drop them.
filterMsLevel: reduces the XCMSnExp object to spectra of the specified MS level(s). Chromatographic peaks and identified features are also subsetted to the respective MS level. See also the filterMsLevel documentation in MSnbase for details and examples.
filterMz: filters the data set based on the provided m/z value range. All chromatographic peaks and features (grouped peaks) with their apex falling within the provided mz value range are retained (i.e. if chromPeaks(object)[, "mz"] is >= mz[1] and <= mz[2]). Adjusted retention times, if present, are kept.
filterRt: filters the data set based on the provided retention time range. All chromatographic peaks and features (grouped peaks) within the specified retention time window are retained (i.e. if the retention time corresponding to the peak's apex is within the specified rt range). If retention time correction has been performed, the method will by default filter the object by adjusted retention times. The argument adjusted allows to specify manually whether filtering should be performed on raw or adjusted retention times. Filtering by retention time does not drop any preprocessing results nor does it remove or change alignment results (i.e. adjusted retention times). The method returns an empty object if no spectrum or feature is within the specified retention time range.
split: splits an XCMSnExp object into a list of XCMSnExp objects based on the provided parameter f. Note that by default all pre-processing results are removed by the splitting, except adjusted retention times, if the optional argument keepAdjustedRtime = TRUE is provided.

Usage

# S4 method for class 'XCMSnExp,ANY,ANY,ANY'
[(x, i, j, ..., drop = TRUE)

# S4 method for class 'XCMSnExp,ANY,ANY'
[[(x, i, j, drop = FALSE)

# S4 method for class 'XCMSnExp'
filterMsLevel(object, msLevel., keepAdjustedRtime = hasAdjustedRtime(object))

# S4 method for class 'XCMSnExp'
filterFile(
  object,
  file,
  keepAdjustedRtime = hasAdjustedRtime(object),
  keepFeatures = FALSE
)

# S4 method for class 'XCMSnExp'
filterMz(object, mz, msLevel., ...)

# S4 method for class 'XCMSnExp'
filterRt(object, rt, msLevel., adjusted = hasAdjustedRtime(object))

# S4 method for class 'XCMSnExp,ANY'
split(x, f, drop = FALSE, ...)

# S4 method for class 'XCMSnExp'
filterChromPeaks(
  object,
  keep = rep(TRUE, nrow(chromPeaks(object))),
  method = "keep",
  ...
)

# S4 method for class 'XCMSnExp'
filterFeatureDefinitions(object, features = integer())

Arguments

x: For [ and [[: an XCMSnExp object.
i: For [: numeric or logical vector specifying to which spectra the data set should be reduced. For [[: a single integer or character.
j: For [ and [[: not supported.
...: Optional additional arguments.
drop: For [ and [[: not supported.
object: A XCMSnExp object.
msLevel.: For filterMz, filterRt: numeric defining the MS level(s) to which operations should be applied or to which the object should be subsetted.
keepAdjustedRtime: For filterFile, filterMsLevel, [, split: logical(1) defining whether the adjusted retention times should be kept, even if e.g. features are being removed (and the retention time correction was performed on these features).
file: For filterFile: integer defining the file index within the object to subset the object by file or character specifying the file names to sub set. The indices are expected to be increasingly ordered, if not they are ordered internally.
keepFeatures: For filterFile: logical(1) whether correspondence results (feature definitions) should be kept or dropped. Defaults to keepFeatures = FALSE hence feature definitions are removed from the returned object by default.
mz: For filterMz: numeric(2) defining the lower and upper mz value for the filtering.
rt: For filterRt: numeric(2) defining the retention time window (lower and upper bound) for the filtering.
adjusted: For filterRt: logical indicating whether the object should be filtered by original (adjusted = FALSE) or adjusted retention times (adjusted = TRUE). For spectra: whether the retention times in the individual Spectrum objects should be the adjusted or raw retention times.
f: For split a vector of length equal to the length of x defining how x should be splitted. It is converted internally to a factor.
keep: For filterChromPeaks: logical, integer or character defining which chromatographic peaks should be retained.
method: For filterChromPeaks: character(1) allowing to specify the method by which chromatographic peaks should be filtered. Currently only method = "keep" is supported (i.e. specify with parameter keep which chromatographic peaks should be retained).
features: For filterFeatureDefinitions: either a integer specifying the indices of the features (rows) to keep, a logical with a length matching the number of rows of featureDefinitions or a character with the feature (row) names.

Value

All methods return an XCMSnExp object.

Details

All subsetting methods try to ensure that the returned data is consistent. Correspondence results for example are removed by default if the data set is sub-setted by file, since the correspondence results are dependent on the files on which correspondence was performed. This can be changed by setting keepFeatures = TRUE. For adjusted retention times, most subsetting methods support the argument keepAdjustedRtime (even the [ method) that forces the adjusted retention times to be retained even if the default would be to drop them.

Note

The filterFile method removes also process history steps not related to the files to which the object should be sub-setted and updates the fileIndex attribute accordingly. Also, the method does not allow arbitrary ordering of the files or re-ordering of the files within the object.

Note also that most of the filtering methods, and also the subsetting operations [ drop all or selected preprocessing results. To consolidate the alignment results, i.e. ensure that adjusted retention times are always preserved, use the applyAdjustedRtime() function on the object that contains the alignment results. This replaces the raw retention times with the adjusted ones.

Author

Johannes Rainer

Examples


## Loading a test data set with identified chromatographic peaks
library(MSnbase)
data(faahko_sub)
## Update the path to the files for the local system
dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")

## Disable parallel processing for this example
register(SerialParam())

## Subset the dataset to the first and third file.
xod_sub <- filterFile(faahko_sub, file = c(1, 3))

## The number of chromatographic peaks per file for the full object
table(chromPeaks(faahko_sub)[, "sample"])
#> 
#>   1   2   3 
#>  87 100  61 

## The number of chromatographic peaks per file for the subset
table(chromPeaks(xod_sub)[, "sample"])
#> 
#>  1  2 
#> 87 61 

basename(fileNames(faahko_sub))
#> [1] "ko15.CDF" "ko16.CDF" "ko18.CDF"
basename(fileNames(xod_sub))
#> [1] "ko15.CDF" "ko18.CDF"

## Filter on mz values; chromatographic peaks and features within the
## mz range are retained (as well as adjusted retention times).
xod_sub <- filterMz(faahko_sub, mz = c(300, 400))
head(chromPeaks(xod_sub))
#>        mz mzmin mzmax       rt    rtmin    rtmax       into       intb   maxo
#> CP002 302   302   302 2617.185 2595.275 2640.659   687146.6   671297.8  30552
#> CP003 344   344   344 2679.783 2646.919 2709.517  5210015.9  5135916.9 152320
#> CP005 366   366   366 2679.783 2642.224 2718.907  3365174.0  3279468.3  79928
#> CP006 343   343   343 2678.218 2637.529 2712.647 24147443.2 23703761.7 672064
#> CP007 365   365   365 2679.783 2634.399 2717.342 14975760.8 14525699.1 357632
#> CP009 313   313   313 2783.070 2768.985 2806.544  1744615.5  1698756.0  74080
#>        sn sample
#> CP002  46      1
#> CP003  68      1
#> CP005  49      1
#> CP006  87      1
#> CP007 111      1
#> CP009  44      1
nrow(chromPeaks(xod_sub))
#> [1] 89
nrow(chromPeaks(faahko_sub))
#> [1] 248

## Filter on rt values. All chromatographic peaks and features within the
## retention time range are retained. Filtering is performed by default on
## adjusted retention times, if present.
xod_sub <- filterRt(faahko_sub, rt = c(2700, 2900))

range(rtime(xod_sub))
#> [1] 2700.127 2898.877
head(chromPeaks(xod_sub))
#>          mz mzmin mzmax       rt    rtmin    rtmax       into       intb   maxo
#> CP008 579.1 579.1 579.1 2786.200 2765.855 2806.544  1669436.8  1642951.6  87656
#> CP009 313.0 313.0 313.0 2783.070 2768.985 2806.544  1744615.5  1698756.0  74080
#> CP010 301.0 301.0 301.0 2786.200 2765.855 2809.674  3051847.8  2958809.7 118512
#> CP011 279.0 279.0 279.0 2787.765 2764.290 2814.369 17140627.0 16526792.4 805248
#> CP012 279.1 279.1 279.1 2825.323 2820.629 2828.453   106769.4   106763.2  17760
#> CP018 453.2 453.2 453.2 2720.472 2678.218 2786.200  2987076.3  2986966.8  34208
#>          sn sample
#> CP008    57      1
#> CP009    44      1
#> CP010    62      1
#> CP011    45      1
#> CP012 17759      1
#> CP018 33983      1
range(chromPeaks(xod_sub)[, "rt"])
#> [1] 2701.693 2895.746

nrow(chromPeaks(faahko_sub))
#> [1] 248
nrow(chromPeaks(xod_sub))
#> [1] 21

## Extract a single Spectrum
faahko_sub[[4]]
#> Object of class "Spectrum1"
#>  Retention time: 41:46 
#>  MSn level: 1 
#>  Total ion count: 427 
#>  Polarity: -1 

## Subsetting using [ removes all preprocessing results - using
## keepAdjustedRtime = TRUE would keep adjusted retention times, if present.
xod_sub <- faahko_sub[fromFile(faahko_sub) == 1]
#> Warning: Removed preprocessing results
xod_sub
#> MSn experiment data ("XCMSnExp")
#> Object size in memory: 0.48 Mb
#> - - - Spectra data - - -
#>  MS level(s): 1 
#>  Number of spectra: 1278 
#>  MSn retention times: 41:41 - 74:60 minutes
#> - - - Processing information - - -
#> Data loaded [Thu Mar 14 11:42:34 2024] 
#>  MSnbase version: 2.29.3 
#> - - - Meta data  - - -
#> phenoData
#>   rowNames: ko15.CDF
#>   varLabels: sampleNames
#>   varMetadata: labelDescription
#> Loaded from:
#>   ko15.CDF 
#> protocolData: none
#> featureData
#>   featureNames: F1.S0001 F1.S0002 ... F1.S1278 (1278 total)
#>   fvarLabels: fileIdx spIdx ... spectrum (35 total)
#>   fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
#> - - - xcms preprocessing - - -

## Using split does also remove preprocessing results, but it supports the
## optional parameter keepAdjustedRtime.
## Split the object into a list of XCMSnExp objects, one per file
xod_list <- split(faahko_sub, f = fromFile(faahko_sub))
xod_list
#> $`1`
#> MSn experiment data ("XCMSnExp")
#> Object size in memory: 0.48 Mb
#> - - - Spectra data - - -
#>  MS level(s): 1 
#>  Number of spectra: 1278 
#>  MSn retention times: 41:41 - 74:60 minutes
#> - - - Processing information - - -
#> Data loaded [Thu Mar 14 11:42:34 2024] 
#>  MSnbase version: 2.29.3 
#> - - - Meta data  - - -
#> phenoData
#>   rowNames: ko15.CDF
#>   varLabels: sampleNames
#>   varMetadata: labelDescription
#> Loaded from:
#>   ko15.CDF 
#> protocolData: none
#> featureData
#>   featureNames: F1.S0001 F1.S0002 ... F1.S1278 (1278 total)
#>   fvarLabels: fileIdx spIdx ... spectrum (35 total)
#>   fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
#> - - - xcms preprocessing - - -
#> 
#> $`2`
#> MSn experiment data ("XCMSnExp")
#> Object size in memory: 0.48 Mb
#> - - - Spectra data - - -
#>  MS level(s): 1 
#>  Number of spectra: 1278 
#>  MSn retention times: 41:41 - 74:60 minutes
#> - - - Processing information - - -
#> Data loaded [Thu Mar 14 11:42:34 2024] 
#>  MSnbase version: 2.29.3 
#> - - - Meta data  - - -
#> phenoData
#>   rowNames: ko16.CDF
#>   varLabels: sampleNames
#>   varMetadata: labelDescription
#> Loaded from:
#>   ko16.CDF 
#> protocolData: none
#> featureData
#>   featureNames: F2.S0001 F2.S0002 ... F2.S1278 (1278 total)
#>   fvarLabels: fileIdx spIdx ... spectrum (35 total)
#>   fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
#> - - - xcms preprocessing - - -
#> 
#> $`3`
#> MSn experiment data ("XCMSnExp")
#> Object size in memory: 0.48 Mb
#> - - - Spectra data - - -
#>  MS level(s): 1 
#>  Number of spectra: 1278 
#>  MSn retention times: 41:41 - 74:60 minutes
#> - - - Processing information - - -
#> Data loaded [Thu Mar 14 11:42:34 2024] 
#>  MSnbase version: 2.29.3 
#> - - - Meta data  - - -
#> phenoData
#>   rowNames: ko18.CDF
#>   varLabels: sampleNames
#>   varMetadata: labelDescription
#> Loaded from:
#>   ko18.CDF 
#> protocolData: none
#> featureData
#>   featureNames: F3.S0001 F3.S0002 ... F3.S1278 (1278 total)
#>   fvarLabels: fileIdx spIdx ... spectrum (35 total)
#>   fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
#> - - - xcms preprocessing - - -
#>