Extract an ion chromatogram for each chromatographic peak

Extract an ion chromatogram (EIC) for each chromatographic peak in an XcmsExperiment() object. Parameters expandRt and expandMz allow to increase the retention time and/or m/z boundaries of each chromatographic peak. Parameter return.type allows to define the format in which the chromatograms are returned:

return.type = "Chromatograms": return the EICs as a Chromatograms::Chromatograms() object. The ID of the chromatographic peak can be accessed with $chrom_peak_id from the returned object.
return.type = "MChromatograms": return the EICs as a (single column) legacy MSnbase::MChromatograms object.
return.type = "XChromatograms": return the EICs as a (single column) legacy XChromatograms() object which contains also the information of all chromatographic peaks.

Usage

chromPeakChromatograms(object, ...)

# S4 method for class 'XcmsExperiment'
chromPeakChromatograms(
  object,
  expandRt = 0,
  expandMz = 0,
  aggregationFun = "max",
  peaks = character(),
  return.type = c("XChromatograms", "MChromatograms", "Chromatograms"),
  ...,
  progressbar = TRUE
)

Arguments

object: An XcmsExperiment() with identified chromatographic peaks.
...: currently ignored.
expandRt: numeric(1) to eventually expand the retention time range from which the signal should be integrated. The chromatogram will contain signal from chromPeaks[, "rtmin"] - expandRt to chromPeaks[, "rtmax"] + expandRt. The default is expandRt = 0.
expandMz: numeric(1) to eventually expand the m/z range from which the signal should be integrated. The chromatogram will contain signal from chromPeaks[, "mzmin"] - expandMz to chromPeaks[, "mzmax"] + expandMz. The default is expandMz = 0.
aggregationFun: character(1) defining the function how signals within the m/z range in each spectrum (i.e. for each discrete retention time) should be aggregated. The default (aggregationFun = "max") reports the largest signal for each spectrum.
peaks: optional character providing the IDs of the chromatographic peaks (i.e. the row names of the peaks in chromPeaks(object)) for which chromatograms should be returned.
return.type: character(1) specifying the type of the returned object. Can be either return.type = "XChromatograms" (the default), return.type = "MChromatograms" or return.type = "Chromatograms".
progressbar: logical(1) whether the progress of the extraction process should be displayed.

Author

Johannes Rainer

Examples


## Load a test data set with detected peaks
library(xcms)
library(MsExperiment)
faahko_sub <- loadXcmsData("faahko_sub2")

## Extract EICs for all chromatographic peaks
library(Chromatograms)
chrs <- chromPeakChromatograms(faahko_sub, return.type = "Chromatograms")
chrs
#> Chromatographic data (Chromatograms) with 248 chromatograms in a ChromBackendSpectra backend:
#>       chromIndex msLevel mz
#> CP001         NA       1 NA
#> CP002         NA       1 NA
#> CP003         NA       1 NA
#> CP004         NA       1 NA
#> CP005         NA       1 NA
#> CP006         NA       1 NA
#> ... 14 more  chromatogram variables/columns
#> ... 2 peaksData variables
#> 
#> The Spectra object contains 3161 spectra

## Get the chrom peak ID of all EICs
chrs$chrom_peak_id
#>   [1] "CP001" "CP002" "CP003" "CP004" "CP005" "CP006" "CP007" "CP008" "CP009"
#>  [10] "CP010" "CP011" "CP012" "CP013" "CP014" "CP015" "CP016" "CP017" "CP018"
#>  [19] "CP019" "CP020" "CP021" "CP022" "CP023" "CP024" "CP025" "CP026" "CP027"
#>  [28] "CP028" "CP029" "CP030" "CP031" "CP032" "CP033" "CP034" "CP035" "CP036"
#>  [37] "CP037" "CP038" "CP039" "CP040" "CP041" "CP042" "CP043" "CP044" "CP045"
#>  [46] "CP046" "CP047" "CP048" "CP049" "CP050" "CP051" "CP052" "CP053" "CP054"
#>  [55] "CP055" "CP056" "CP057" "CP058" "CP059" "CP060" "CP061" "CP062" "CP063"
#>  [64] "CP064" "CP065" "CP066" "CP067" "CP068" "CP069" "CP070" "CP071" "CP072"
#>  [73] "CP073" "CP074" "CP075" "CP076" "CP077" "CP078" "CP079" "CP080" "CP081"
#>  [82] "CP082" "CP083" "CP084" "CP085" "CP086" "CP087" "CP088" "CP089" "CP090"
#>  [91] "CP091" "CP092" "CP093" "CP094" "CP095" "CP096" "CP097" "CP098" "CP099"
#> [100] "CP100" "CP101" "CP102" "CP103" "CP104" "CP105" "CP106" "CP107" "CP108"
#> [109] "CP109" "CP110" "CP111" "CP112" "CP113" "CP114" "CP115" "CP116" "CP117"
#> [118] "CP118" "CP119" "CP120" "CP121" "CP122" "CP123" "CP124" "CP125" "CP126"
#> [127] "CP127" "CP128" "CP129" "CP130" "CP131" "CP132" "CP133" "CP134" "CP135"
#> [136] "CP136" "CP137" "CP138" "CP139" "CP140" "CP141" "CP142" "CP143" "CP144"
#> [145] "CP145" "CP146" "CP147" "CP148" "CP149" "CP150" "CP151" "CP152" "CP153"
#> [154] "CP154" "CP155" "CP156" "CP157" "CP158" "CP159" "CP160" "CP161" "CP162"
#> [163] "CP163" "CP164" "CP165" "CP166" "CP167" "CP168" "CP169" "CP170" "CP171"
#> [172] "CP172" "CP173" "CP174" "CP175" "CP176" "CP177" "CP178" "CP179" "CP180"
#> [181] "CP181" "CP182" "CP183" "CP184" "CP185" "CP186" "CP187" "CP188" "CP189"
#> [190] "CP190" "CP191" "CP192" "CP193" "CP194" "CP195" "CP196" "CP197" "CP198"
#> [199] "CP199" "CP200" "CP201" "CP202" "CP203" "CP204" "CP205" "CP206" "CP207"
#> [208] "CP208" "CP209" "CP210" "CP211" "CP212" "CP213" "CP214" "CP215" "CP216"
#> [217] "CP217" "CP218" "CP219" "CP220" "CP221" "CP222" "CP223" "CP224" "CP225"
#> [226] "CP226" "CP227" "CP228" "CP229" "CP230" "CP231" "CP232" "CP233" "CP234"
#> [235] "CP235" "CP236" "CP237" "CP238" "CP239" "CP240" "CP241" "CP242" "CP243"
#> [244] "CP244" "CP245" "CP246" "CP247" "CP248"

## Plot the first 4 EICs
plotChromatograms(chrs[1:4])


## Plot the first 4 EICs into the same plot
plotChromatogramsOverlay(chrs[1:4])

## Use the legacy EIC infrastructure (MChromatograms, XChromatograms)
library(MSnbase)
## Get EICs for every detected chromatographic peak
chrs <- chromPeakChromatograms(faahko_sub)
chrs
#> XChromatograms with 248 rows and 1 column
#>                   [,1]
#>        <XChromatogram>
#> [1,]          peaks: 1
#> [2,]          peaks: 1
#> ...               ... 
#> [247,]        peaks: 1
#> [248,]        peaks: 1
#> phenoData with 2 variables
#> featureData with 5 variables
#> - - - xcms preprocessing - - -
#> Chromatographic peak detection:
#>  method: centWave 

## Order of EICs matches the order in chromPeaks
chromPeaks(faahko_sub) |> head()
#>          mz mzmin mzmax       rt    rtmin    rtmax       into       intb   maxo
#> CP001 453.2 453.2 453.2 2506.073 2501.378 2527.982  1007409.0  1007380.8  38152
#> CP002 302.0 302.0 302.0 2617.185 2595.275 2640.659   687146.6   671297.8  30552
#> CP003 344.0 344.0 344.0 2679.783 2646.919 2709.517  5210015.9  5135916.9 152320
#> CP004 430.1 430.1 430.1 2681.348 2639.094 2712.647  2395840.3  2299899.6  65752
#> CP005 366.0 366.0 366.0 2679.783 2642.224 2718.907  3365174.0  3279468.3  79928
#> CP006 343.0 343.0 343.0 2678.218 2637.529 2712.647 24147443.2 23703761.7 672064
#>          sn sample
#> CP001 38151      1
#> CP002    46      1
#> CP003    68      1
#> CP004    42      1
#> CP005    49      1
#> CP006    87      1

## variable "sample_index" provides the index of the sample the EIC was
## extracted from
fData(chrs)$sample_index
#>   [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#>  [38] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#>  [75] 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
#> [112] 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 2 2 2 2 2 2 2 2 2 2 2 2
#> [149] 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 2 2 2 2 2 2 2 2 2 2 2 2
#> [186] 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
#> [223] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3

## Get the EIC for selected peaks only.
pks <- rownames(chromPeaks(faahko_sub))[c(6, 12)]
pks
#> [1] "CP006" "CP012"

## Expand the data on retention time dimension by 15 seconds (on each side)
res <- chromPeakChromatograms(faahko_sub, peaks = pks, expandRt = 5)
plot(res[1, ])

Extract an ion chromatogram for each chromatographic peak

Usage

Arguments

See also

Author

Examples