R/AllClasses.R, R/methods-AbstractTopDownSet.R
AbstractTopDownSet-class.RdAbstract/VIRTUAL parent class for TopDownSet and NCBSet to provide common interface.
# S4 method for AbstractTopDownSet,ANY,ANY,ANY
[(x, i, j, ..., drop = FALSE)
# S4 method for AbstractTopDownSet,ANY,missing
[[(x, i, j, ...)
# S4 method for AbstractTopDownSet,ANY,missing
[[(x, i, j, ...) <- value
# S4 method for AbstractTopDownSet
$(x, name)
# S4 method for AbstractTopDownSet
$(x, name) <- value
# S4 method for AbstractTopDownSet
assayData(object)
# S4 method for AbstractTopDownSet
colData(object)
# S4 method for AbstractTopDownSet
colData(object, ...) <- value
# S4 method for AbstractTopDownSet,AbstractTopDownSet
combine(x, y)
# S4 method for AbstractTopDownSet
conditionData(object, ...)
# S4 method for AbstractTopDownSet
conditionData(object, ...) <- value
# S4 method for AbstractTopDownSet
conditionNames(object)
# S4 method for AbstractTopDownSet
dim(x)
# S4 method for AbstractTopDownSet
dimnames(x)
# S4 method for AbstractTopDownSet
removeEmptyConditions(object)
# S4 method for AbstractTopDownSet
rowViews(object, ...)
# S4 method for AbstractTopDownSet
show(object)
# S4 method for AbstractTopDownSet
summary(object, what = c("rows", "columns"), ...)
# S4 method for AbstractTopDownSet
updateConditionNames(
object,
sampleColumns = c("Mz", "AgcTarget", "EtdReagentTarget", "EtdActivation",
"CidActivation", "HcdActivation", "UvpdActivation"),
verbose = interactive()
)
# S4 method for AbstractTopDownSet
updateMedianInjectionTime(
object,
by = list(Mz = object$Mz, AgcTarget = object$AgcTarget)
)| i, j |
|
|---|---|
| drop |
|
| value | replacment value. |
| name |
|
| object, x |
|
| y |
|
| what |
|
| sampleColumns |
|
| verbose |
|
| by |
|
| ... | arguments passed to internal/other methods. |
This is an Abstract/VIRTUAL class
to provide a common interface for
TopDownSet and NCBSet.
It is not possible to create an AbstractTopDownSet object.
This class just provides a common interface. It is not intended for direct use by the user. Please see TopDownSet for an example usage of its child class.
[: Subset operator.
For i numeric, logical or character vectors or empty
(missing) or NULL are supported.
Subsetting is done on the fragment/bond (row) level.
character indices could be names
(e.g. c("a1", "b1", "c1", "c2", "c3"))
or types (e.g. c("c", "x")) of the fragments for
TopDownSet objects,
or names of the bonds (e.g. c("bond001")) for
NCBSet objects.
j could be a numeric or logical vector
and subsetting is done on the condition/run (column) level.
[[: Subset operator.
i could be a numeric or logical vector and
subsetting is done on the condition/run (column) level.
[[<-: Setter for a column in the colData slot.
The [[<- operator is used to add/replace
a single column of the colData DataFrame.
$: Accessor for columns in the colData slot.
The $ simplifies the accession of a single column
of the colData.
It is identical to the [[ operator.
$<-: Setter for a column in the colData slot.
The $<- operator is used to add/replace a single column
of the colData DataFrame.
It is identical to the [[<- operator.
assayData: Accessor for the assay slot.
Returns a Matrix::dgCMatrix that stores the intensity/coverage information of AbstractTopDownSet object.
colData: Accessor for the colData slot.
Returns a S4Vectors::DataFrame that stores metadata for the conditons/runs (columns) of the AbstractTopDownSet object.
colData<-: Setter for the colData slot.
Replaces metadata for the conditons/runs (columns) of the AbstractTopDownSet object.
combine: Combine AbstractTopDownSet objects.
combine allows to combine two or more AbstractTopDownSet objects.
Please note that it uses the default
sampleColumns to define technical replicates (see readTopDownFiles()).and
the default by argument to group ion injection times for the calculation of
the median time (see updateMedianInjectionTime()). Both could be modified
after combine by calling updateConditionNames() (with modified
sampleColumns argument) and updateMedianInjectionTime() (with modified
by argument).
conditionData: Accessor for the colData slot.
An alias for colData.
conditionData<-: Setter for the colData slot.
An alias for colData<-.
conditionNames: Accessor for condition names.
Returns a character with names for the conditions/runs (columns).
dim: Accessor for dimensions.
Returns a numeric with number of fragments/bonds (rows) and
conditions/runs (columns).
dimnames: Accessor for dimension names.
Returns a list with names for the fragments/bonds (rows) and for the
conditions/runs (columns).
removeEmptyConditions: Remove empty conditions/runs.
Removes conditions/runs (columns) without any intensity/coverage information from the AbstractTopDownSet object. It returns a modified AbstractTopDownSet object.
rowViews: Accessor for the rowViews slot.
Depending on the implementation it returns an FragmentViews object for TopDownSet objects or an Biostrings::XStringViews object for NCBSet objects.
summary: Summary statistics.
Returns a matrix with some statistics: number of fragments,
total/min/first quartile/median/mean/third quartile/maximum of intensity
values.
updateConditionNames: Update condition names.
Updates condition names based on sampleColumns from
conditionData/colData. Columns with just identical entries are ignored.
This method will create/update the colData(object)$Sample column that
identifies technical replicates and could be used in other methods.
updateMedianInjectionTime: Update median ion injection times.
Recalculates median ion injection times by a user given grouping variable
(default: Mz, AgcTarget). This is useful if you acquire new data and the ion
injection time differs across the runs. Use the by argument to provide a
list/data.frame of grouping variables, e.g.
by=colData(object)[, c("Mz", "AgcTarget", "File")].
rowViewsBiostrings::XStringViews, information about fragments/bonds (name, type, sequence, mass, charge), see Biostrings::XStringViews and FragmentViews for details.
colDataS4Vectors::DataFrame, information about the MS2 experiments and the fragmentation conditions.
assayMatrix::dgCMatrix, intensity/coverage values of the fragments/bonds. The rows correspond to the fragments/bonds and the columns to the condition/run. It just stores values that are different from zero.
filescharacter, files that were imported.
processingcharacter, log messages.
TopDownSet and NCBSet which both implement/use this interface. These manual pages also provide some example code.
FragmentViews (and Biostrings::XStringViews) for the row view interface.
Matrix::dgCMatrix for technical details about the intensity/coverage storage.
Sebastian Gibb mail@sebastiangibb.de
## Because AbstractTopDownSet is a VIRTUAL class we could not create any
## object of it. Here we demonstrate the usage with an TopDownSet that
## implements the AbstractTopDownSet interface. See `?"TopDownSet-class"` for
## more details an further examples.
## Example data
data(tds, package="topdownr")
tds
#> TopDownSet object (0.72 Mb)
#> - - - Protein data - - -
#> Amino acid sequence (153): GLSDGEWQQVLNVWGKVEADIAGHGQ...GAMTKALELFRNDIAAKYKELGFQG
#> Mass : 16964.96
#> Modifications (3): Carbamidomethyl, Acetyl, Met-loss
#> - - - Fragment data - - -
#> Number of theoretical fragments: 1949
#> Theoretical fragment types (12): a, a*, b, b*, c, ..., x*, y, y*, z, z*
#> Theoretical mass range: [72.04;16925.98]
#> - - - Condition data - - -
#> Number of conditions: 222
#> Number of scans: 351
#> Condition variables (59): File, Scan, ..., Sample, MedianIonInjectionTimeMs
#> - - - Intensity data - - -
#> Size of array: 1949x351 (2.12% != 0)
#> Number of matched fragments: 14518
#> Intensity range: [126.42;1454253.25]
#> - - - Processing information - - -
#> [2018-01-30 11:39:16] 14518 fragments [1949;351] matched (tolerance: 25 ppm, strategies ion/fragment: remove/remove).
#> [2018-01-30 11:39:16] Condition names updated based on: Mz, AgcTarget, EtdReagentTarget, EtdActivation, CidActivation, HcdActivation. Order of conditions changed. 222 conditions.
#> [2018-01-30 11:39:16] Recalculate median injection time based on: Mz, AgcTarget.
head(summary(tds))
#> Fragments Total Min Q1 Median
#> C1.0e+05_1.0e+06_02.50_07_00_1 48 3350602 5289.57 14243.25 31047.62
#> C1.0e+05_1.0e+06_02.50_07_00_2 46 3352669 3147.54 17875.76 29926.68
#> C1.0e+05_1.0e+06_02.50_14_00_1 46 3204442 3842.46 17372.92 29012.01
#> C1.0e+05_1.0e+06_02.50_14_00_2 48 3320782 3848.07 11656.87 32890.28
#> C1.0e+05_1.0e+06_02.50_21_00 57 3590927 3787.77 12579.74 27829.12
#> C1.0e+05_1.0e+06_02.50_28_00_1 58 3291440 1843.09 10398.68 21424.32
#> Mean Q3 Max
#> C1.0e+05_1.0e+06_02.50_07_00_1 1719.139 59497.87 607970.2
#> C1.0e+05_1.0e+06_02.50_07_00_2 1720.199 73423.75 641441.3
#> C1.0e+05_1.0e+06_02.50_14_00_1 1644.147 68124.07 669750.9
#> C1.0e+05_1.0e+06_02.50_14_00_2 1703.839 54575.39 601565.8
#> C1.0e+05_1.0e+06_02.50_21_00 1842.446 51986.04 607209.7
#> C1.0e+05_1.0e+06_02.50_28_00_1 1688.784 48499.72 589361.6
# Accessing slots
rowViews(tds)
#> FragmentViews on a 153-letter sequence:
#> GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPE...SKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG
#> Mass:
#> 16964.964625
#> Modifications:
#> Carbamidomethyl
#> Acetyl
#> Met-loss
#> Views:
#> start end width mass name type z
#> [1] 1 1 1 72.04 a1 a 1 [G]
#> [2] 1 1 1 100.04 b1 b 1 [G]
#> [3] 1 1 1 101.02 z1 z 1 [G]
#> [4] 1 1 1 102.03 zpH1 z 1 [G]
#> [5] 1 1 1 117.07 c1 c 1 [G]
#> ... ... ... ... ... ... ... ... ...
#> [1945] 2 153 152 16893.90 x152* x* 1 [LSDGEWQQVLNVWG...NDIAAKYKELGFQG]
#> [1946] 1 152 152 16908.95 b152 b 1 [GLSDGEWQQVLNVW...RNDIAAKYKELGFQ]
#> [1947] 1 152 152 16908.95 c152* c* 1 [GLSDGEWQQVLNVW...RNDIAAKYKELGFQ]
#> [1948] 2 153 152 16910.93 x152 x 1 [LSDGEWQQVLNVWG...NDIAAKYKELGFQG]
#> [1949] 1 152 152 16925.98 c152 c 1 [GLSDGEWQQVLNVW...RNDIAAKYKELGFQ]
colData(tds)
#> DataFrame with 351 rows and 59 columns
#> File Scan SpectrumIndex
#> <Rle> <integer> <integer>
#> C1.0e+05_1.0e+06_02.50_07_00_1 myo_1211_ETDReagentT.. 33 23
#> C1.0e+05_1.0e+06_02.50_07_00_2 myo_1211_ETDReagentT.. 34 24
#> C1.0e+05_1.0e+06_02.50_14_00_1 myo_1211_ETDReagentT.. 36 26
#> C1.0e+05_1.0e+06_02.50_14_00_2 myo_1211_ETDReagentT.. 37 27
#> C1.0e+05_1.0e+06_02.50_21_00 myo_1211_ETDReagentT.. 40 30
#> ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 myo_1211_ETDReagentT.. 265 249
#> C1.0e+06_0.0e+00_00.00_00_28_1 myo_1211_ETDReagentT.. 268 252
#> C1.0e+06_0.0e+00_00.00_00_28_2 myo_1211_ETDReagentT.. 269 253
#> C1.0e+06_0.0e+00_00.00_00_35_1 myo_1211_ETDReagentT.. 271 255
#> C1.0e+06_0.0e+00_00.00_00_35_2 myo_1211_ETDReagentT.. 272 256
#> PeaksCount TotIonCurrent RetentionTime
#> <integer> <numeric> <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1 135 13727530 371.466
#> C1.0e+05_1.0e+06_02.50_07_00_2 133 14978619 389.412
#> C1.0e+05_1.0e+06_02.50_14_00_1 124 15124274 425.397
#> C1.0e+05_1.0e+06_02.50_14_00_2 144 14001930 443.256
#> C1.0e+05_1.0e+06_02.50_21_00 148 14008273 497.289
#> ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 471 3388050 4764.55
#> C1.0e+06_0.0e+00_00.00_00_28_1 233 2060326 4814.02
#> C1.0e+06_0.0e+00_00.00_00_28_2 172 1970904 4830.14
#> C1.0e+06_0.0e+00_00.00_00_35_1 166 2918202 4863.09
#> C1.0e+06_0.0e+00_00.00_00_35_2 231 2861092 4878.68
#> BasePeakMz BasePeakIntensity.SpectraInformation
#> <numeric> <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1 16943 4631841
#> C1.0e+05_1.0e+06_02.50_07_00_2 16943 5103187
#> C1.0e+05_1.0e+06_02.50_14_00_1 16943 5346571
#> C1.0e+05_1.0e+06_02.50_14_00_2 16943 4668278
#> C1.0e+05_1.0e+06_02.50_21_00 16943 4605146
#> ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 231.123 56502.7
#> C1.0e+06_0.0e+00_00.00_00_28_1 231.123 96439.5
#> C1.0e+06_0.0e+00_00.00_00_28_2 231.123 104296.8
#> C1.0e+06_0.0e+00_00.00_00_35_1 231.123 261401.5
#> C1.0e+06_0.0e+00_00.00_00_35_2 231.123 238047.0
#> LowMz HighMz PrecursorMz
#> <numeric> <numeric> <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1 762.391 17146.1 1211.7
#> C1.0e+05_1.0e+06_02.50_07_00_2 762.390 17146.1 1211.7
#> C1.0e+05_1.0e+06_02.50_14_00_1 762.391 17146.1 1211.7
#> C1.0e+05_1.0e+06_02.50_14_00_2 762.391 17146.1 1211.7
#> C1.0e+05_1.0e+06_02.50_21_00 762.391 17146.1 1211.7
#> ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 200.139 5970.087 1211.72
#> C1.0e+06_0.0e+00_00.00_00_28_1 200.139 1460.807 1211.72
#> C1.0e+06_0.0e+00_00.00_00_28_2 200.139 1351.744 1211.72
#> C1.0e+06_0.0e+00_00.00_00_35_1 200.139 959.491 1211.72
#> C1.0e+06_0.0e+00_00.00_00_35_2 200.139 1138.667 1211.72
#> SpectrumId Condition
#> <character> <integer>
#> C1.0e+05_1.0e+06_02.50_07_00_1 controllerType=0 con.. 12
#> C1.0e+05_1.0e+06_02.50_07_00_2 controllerType=0 con.. 12
#> C1.0e+05_1.0e+06_02.50_14_00_1 controllerType=0 con.. 14
#> C1.0e+05_1.0e+06_02.50_14_00_2 controllerType=0 con.. 14
#> C1.0e+05_1.0e+06_02.50_21_00 controllerType=0 con.. 16
#> ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 controllerType=0 con.. 158
#> C1.0e+06_0.0e+00_00.00_00_28_1 controllerType=0 con.. 160
#> C1.0e+06_0.0e+00_00.00_00_28_2 controllerType=0 con.. 160
#> C1.0e+06_0.0e+00_00.00_00_35_1 controllerType=0 con.. 162
#> C1.0e+06_0.0e+00_00.00_00_35_2 controllerType=0 con.. 162
#> FilterString.HeaderInformation
#> <character>
#> C1.0e+05_1.0e+06_02.50_07_00_1 FTMS + p NSI sa Full..
#> C1.0e+05_1.0e+06_02.50_07_00_2 FTMS + p NSI sa Full..
#> C1.0e+05_1.0e+06_02.50_14_00_1 FTMS + p NSI sa Full..
#> C1.0e+05_1.0e+06_02.50_14_00_2 FTMS + p NSI sa Full..
#> C1.0e+05_1.0e+06_02.50_21_00 FTMS + p NSI sa Full..
#> ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 FTMS + p NSI Full ms..
#> C1.0e+06_0.0e+00_00.00_00_28_1 FTMS + p NSI Full ms..
#> C1.0e+06_0.0e+00_00.00_00_28_2 FTMS + p NSI Full ms..
#> C1.0e+06_0.0e+00_00.00_00_35_1 FTMS + p NSI Full ms..
#> C1.0e+06_0.0e+00_00.00_00_35_2 FTMS + p NSI Full ms..
#> SupplementalActivation RtMin Tic
#> <Rle> <numeric> <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1 TRUE 6.19109 159451792
#> C1.0e+05_1.0e+06_02.50_07_00_2 TRUE 6.49019 171593248
#> C1.0e+05_1.0e+06_02.50_14_00_1 TRUE 7.08995 178472720
#> C1.0e+05_1.0e+06_02.50_14_00_2 TRUE 7.38760 159089344
#> C1.0e+05_1.0e+06_02.50_21_00 TRUE 8.28815 159144752
#> ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 FALSE 79.4093 6983628
#> C1.0e+06_0.0e+00_00.00_00_28_1 FALSE 80.2337 4512664
#> C1.0e+06_0.0e+00_00.00_00_28_2 FALSE 80.5023 4734344
#> C1.0e+06_0.0e+00_00.00_00_35_1 FALSE 81.0515 6846192
#> C1.0e+06_0.0e+00_00.00_00_35_2 FALSE 81.3113 6351402
#> BasePeakPosition
#> <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1 1304.93
#> C1.0e+05_1.0e+06_02.50_07_00_2 1304.93
#> C1.0e+05_1.0e+06_02.50_14_00_1 1304.93
#> C1.0e+05_1.0e+06_02.50_14_00_2 1304.93
#> C1.0e+05_1.0e+06_02.50_21_00 1304.93
#> ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 231.123
#> C1.0e+06_0.0e+00_00.00_00_28_1 231.123
#> C1.0e+06_0.0e+00_00.00_00_28_2 159.091
#> C1.0e+06_0.0e+00_00.00_00_35_1 231.123
#> C1.0e+06_0.0e+00_00.00_00_35_2 231.123
#> BasePeakIntensity.HeaderInformation
#> <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1 3762917
#> C1.0e+05_1.0e+06_02.50_07_00_2 3784709
#> C1.0e+05_1.0e+06_02.50_14_00_1 3987072
#> C1.0e+05_1.0e+06_02.50_14_00_2 3722252
#> C1.0e+05_1.0e+06_02.50_21_00 3627429
#> ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 50586.9
#> C1.0e+06_0.0e+00_00.00_00_28_1 86218.9
#> C1.0e+06_0.0e+00_00.00_00_28_2 113096.1
#> C1.0e+06_0.0e+00_00.00_00_35_1 232769.3
#> C1.0e+06_0.0e+00_00.00_00_35_2 212045.9
#> IonInjectionTimeMs ElapsedScanTimeSec HcdEnergy
#> <numeric> <numeric> <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1 5.594 17.883 NA
#> C1.0e+05_1.0e+06_02.50_07_00_2 3.844 17.817 NA
#> C1.0e+05_1.0e+06_02.50_14_00_1 3.345 17.796 NA
#> C1.0e+05_1.0e+06_02.50_14_00_2 5.548 17.885 NA
#> C1.0e+05_1.0e+06_02.50_21_00 5.622 17.887 NA
#> ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 33.946 15.801 21
#> C1.0e+06_0.0e+00_00.00_00_28_1 40.343 16.056 28
#> C1.0e+06_0.0e+00_00.00_00_28_2 26.210 15.493 28
#> C1.0e+06_0.0e+00_00.00_00_35_1 27.029 15.523 35
#> C1.0e+06_0.0e+00_00.00_00_35_2 41.227 16.093 35
#> ConversionParameterB ConversionParameterC
#> <Rle> <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1 211703103.257927 -146989183.520749
#> C1.0e+05_1.0e+06_02.50_07_00_2 211703103.257927 -146989183.520749
#> C1.0e+05_1.0e+06_02.50_14_00_1 211703102.662952 -146989182.69859
#> C1.0e+05_1.0e+06_02.50_14_00_2 211703102.662952 -146989182.69859
#> C1.0e+05_1.0e+06_02.50_21_00 211703102.056363 -146989181.8545
#> ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 211702381.311807 -146988181.00019
#> C1.0e+06_0.0e+00_00.00_00_28_1 211702380.623441 -146988180.050792
#> C1.0e+06_0.0e+00_00.00_00_28_2 211702380.623441 -146988180.050792
#> C1.0e+06_0.0e+00_00.00_00_35_1 211702379.937029 -146988179.095817
#> C1.0e+06_0.0e+00_00.00_00_35_2 211702379.937029 -146988179.095817
#> TemperatureCompPpm SpaceChargeCompPpm RawOvFtt
#> <Rle> <Rle> <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1 -14.44 -0.18 889335
#> C1.0e+05_1.0e+06_02.50_07_00_2 -14.44 -0.18 667089
#> C1.0e+05_1.0e+06_02.50_14_00_1 -14.44 -0.18 603503
#> C1.0e+05_1.0e+06_02.50_14_00_2 -14.44 -0.18 889291
#> C1.0e+05_1.0e+06_02.50_21_00 -14.44 -0.18 897244
#> ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 -14.56 -1.76 247569
#> C1.0e+06_0.0e+00_00.00_00_28_1 -14.56 -1.76 187648
#> C1.0e+06_0.0e+00_00.00_00_28_2 -14.56 -1.76 130142
#> C1.0e+06_0.0e+00_00.00_00_35_1 -14.56 -1.76 191043
#> C1.0e+06_0.0e+00_00.00_00_35_2 -14.56 -1.76 268899
#> InjectionT0 NrCentroids SelectedMass1
#> <numeric> <integer> <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1 0 3513 1211.7
#> C1.0e+05_1.0e+06_02.50_07_00_2 0 3053 1211.7
#> C1.0e+05_1.0e+06_02.50_14_00_1 0 3114 1211.7
#> C1.0e+05_1.0e+06_02.50_14_00_2 0 3743 1211.7
#> C1.0e+05_1.0e+06_02.50_21_00 0 3629 1211.7
#> ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 -0.054 4686 1211.72
#> C1.0e+06_0.0e+00_00.00_00_28_1 0.021 2640 1211.72
#> C1.0e+06_0.0e+00_00.00_00_28_2 0.045 2052 1211.72
#> C1.0e+06_0.0e+00_00.00_00_35_1 0.034 2123 1211.72
#> C1.0e+06_0.0e+00_00.00_00_35_2 0.036 2608 1211.72
#> Activation1 Energy1 SelectedMass2 Activation2
#> <Rle> <Rle> <Rle> <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1 ETD 2.5 0 CID
#> C1.0e+05_1.0e+06_02.50_07_00_2 ETD 2.5 0 CID
#> C1.0e+05_1.0e+06_02.50_14_00_1 ETD 2.5 0 CID
#> C1.0e+05_1.0e+06_02.50_14_00_2 ETD 2.5 0 CID
#> C1.0e+05_1.0e+06_02.50_21_00 ETD 2.5 0 CID
#> ... ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 HCD 21 NA NA
#> C1.0e+06_0.0e+00_00.00_00_28_1 HCD 28 NA NA
#> C1.0e+06_0.0e+00_00.00_00_28_2 HCD 28 NA NA
#> C1.0e+06_0.0e+00_00.00_00_35_1 HCD 35 NA NA
#> C1.0e+06_0.0e+00_00.00_00_35_2 HCD 35 NA NA
#> Energy2 EtdActivation CidActivation
#> <Rle> <Rle> <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1 7 2.5 7
#> C1.0e+05_1.0e+06_02.50_07_00_2 7 2.5 7
#> C1.0e+05_1.0e+06_02.50_14_00_1 14 2.5 14
#> C1.0e+05_1.0e+06_02.50_14_00_2 14 2.5 14
#> C1.0e+05_1.0e+06_02.50_21_00 21 2.5 21
#> ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 NA NA NA
#> C1.0e+06_0.0e+00_00.00_00_28_1 NA NA NA
#> C1.0e+06_0.0e+00_00.00_00_28_2 NA NA NA
#> C1.0e+06_0.0e+00_00.00_00_35_1 NA NA NA
#> C1.0e+06_0.0e+00_00.00_00_35_2 NA NA NA
#> HcdActivation Activation StartTime EndTime
#> <Rle> <Rle> <numeric> <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1 NA ETcid 6.01 6.5
#> C1.0e+05_1.0e+06_02.50_07_00_2 NA ETcid 6.01 6.5
#> C1.0e+05_1.0e+06_02.50_14_00_1 NA ETcid 7.01 7.5
#> C1.0e+05_1.0e+06_02.50_14_00_2 NA ETcid 7.01 7.5
#> C1.0e+05_1.0e+06_02.50_21_00 NA ETcid 8.01 8.5
#> ... ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 21 HCD 79.01 79.5
#> C1.0e+06_0.0e+00_00.00_00_28_1 28 HCD 80.01 80.5
#> C1.0e+06_0.0e+00_00.00_00_28_2 28 HCD 80.01 80.5
#> C1.0e+06_0.0e+00_00.00_00_35_1 35 HCD 81.01 81.5
#> C1.0e+06_0.0e+00_00.00_00_35_2 35 HCD 81.01 81.5
#> ActivationType Ce SteppedCe SteppedCeValue
#> <Rle> <Rle> <Rle> <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1 ETD NA NA
#> C1.0e+05_1.0e+06_02.50_07_00_2 ETD NA NA
#> C1.0e+05_1.0e+06_02.50_14_00_1 ETD NA NA
#> C1.0e+05_1.0e+06_02.50_14_00_2 ETD NA NA
#> C1.0e+05_1.0e+06_02.50_21_00 ETD NA NA
#> ... ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 HCD 25 False 5
#> C1.0e+06_0.0e+00_00.00_00_28_1 HCD 25 False 5
#> C1.0e+06_0.0e+00_00.00_00_28_2 HCD 25 False 5
#> C1.0e+06_0.0e+00_00.00_00_35_1 HCD 25 False 5
#> C1.0e+06_0.0e+00_00.00_00_35_2 HCD 25 False 5
#> MultistageActivation Ethcd
#> <Rle> <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1 FALSE
#> C1.0e+05_1.0e+06_02.50_07_00_2 FALSE
#> C1.0e+05_1.0e+06_02.50_14_00_1 FALSE
#> C1.0e+05_1.0e+06_02.50_14_00_2 FALSE
#> C1.0e+05_1.0e+06_02.50_21_00 FALSE
#> ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 FALSE
#> C1.0e+06_0.0e+00_00.00_00_28_1 FALSE
#> C1.0e+06_0.0e+00_00.00_00_28_2 FALSE
#> C1.0e+06_0.0e+00_00.00_00_35_1 FALSE
#> C1.0e+06_0.0e+00_00.00_00_35_2 FALSE
#> UseCalibratedEtdParameters EtdReactionTime
#> <Rle> <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1 False 2.5
#> C1.0e+05_1.0e+06_02.50_07_00_2 False 2.5
#> C1.0e+05_1.0e+06_02.50_14_00_1 False 2.5
#> C1.0e+05_1.0e+06_02.50_14_00_2 False 2.5
#> C1.0e+05_1.0e+06_02.50_21_00 False 2.5
#> ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 NA
#> C1.0e+06_0.0e+00_00.00_00_28_1 NA
#> C1.0e+06_0.0e+00_00.00_00_28_2 NA
#> C1.0e+06_0.0e+00_00.00_00_35_1 NA
#> C1.0e+06_0.0e+00_00.00_00_35_2 NA
#> EtdReagentTarget EtdSupplementalActivation
#> <Rle> <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1 1000000 True
#> C1.0e+05_1.0e+06_02.50_07_00_2 1000000 True
#> C1.0e+05_1.0e+06_02.50_14_00_1 1000000 True
#> C1.0e+05_1.0e+06_02.50_14_00_2 1000000 True
#> C1.0e+05_1.0e+06_02.50_21_00 1000000 True
#> ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 NA
#> C1.0e+06_0.0e+00_00.00_00_28_1 NA
#> C1.0e+06_0.0e+00_00.00_00_28_2 NA
#> C1.0e+06_0.0e+00_00.00_00_35_1 NA
#> C1.0e+06_0.0e+00_00.00_00_35_2 NA
#> SupplementalActivationCe AgcTarget Activationq
#> <Rle> <Rle> <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1 7 100000 NA
#> C1.0e+05_1.0e+06_02.50_07_00_2 7 100000 NA
#> C1.0e+05_1.0e+06_02.50_14_00_1 14 100000 NA
#> C1.0e+05_1.0e+06_02.50_14_00_2 14 100000 NA
#> C1.0e+05_1.0e+06_02.50_21_00 21 100000 NA
#> ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 NA 1000000 NA
#> C1.0e+06_0.0e+00_00.00_00_28_1 NA 1000000 NA
#> C1.0e+06_0.0e+00_00.00_00_28_2 NA 1000000 NA
#> C1.0e+06_0.0e+00_00.00_00_35_1 NA 1000000 NA
#> C1.0e+06_0.0e+00_00.00_00_35_2 NA 1000000 NA
#> TargetedMassList Mz Charge Sample
#> <character> <Rle> <Rle> <integer>
#> C1.0e+05_1.0e+06_02.50_07_00_1 (mz=1211.7012 z=1 na.. 1211.7 14 1
#> C1.0e+05_1.0e+06_02.50_07_00_2 (mz=1211.7012 z=1 na.. 1211.7 14 1
#> C1.0e+05_1.0e+06_02.50_14_00_1 (mz=1211.7014 z=1 na.. 1211.7 14 2
#> C1.0e+05_1.0e+06_02.50_14_00_2 (mz=1211.7014 z=1 na.. 1211.7 14 2
#> C1.0e+05_1.0e+06_02.50_21_00 (mz=1211.7016 z=1 na.. 1211.7 14 3
#> ... ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 (mz=1211.7158 z=1 na.. 1211.7 14 220
#> C1.0e+06_0.0e+00_00.00_00_28_1 (mz=1211.716 z=1 nam.. 1211.7 14 221
#> C1.0e+06_0.0e+00_00.00_00_28_2 (mz=1211.716 z=1 nam.. 1211.7 14 221
#> C1.0e+06_0.0e+00_00.00_00_35_1 (mz=1211.7162 z=1 na.. 1211.7 14 222
#> C1.0e+06_0.0e+00_00.00_00_35_2 (mz=1211.7162 z=1 na.. 1211.7 14 222
#> MedianIonInjectionTimeMs
#> <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1 4.837
#> C1.0e+05_1.0e+06_02.50_07_00_2 4.837
#> C1.0e+05_1.0e+06_02.50_14_00_1 4.837
#> C1.0e+05_1.0e+06_02.50_14_00_2 4.837
#> C1.0e+05_1.0e+06_02.50_21_00 4.837
#> ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 43.14
#> C1.0e+06_0.0e+00_00.00_00_28_1 43.14
#> C1.0e+06_0.0e+00_00.00_00_28_2 43.14
#> C1.0e+06_0.0e+00_00.00_00_35_1 43.14
#> C1.0e+06_0.0e+00_00.00_00_35_2 43.14
head(assayData(tds))
#> 6 x 351 sparse Matrix of class "dgCMatrix"
#> [[ suppressing 351 column names ‘C1.0e+05_1.0e+06_02.50_07_00_1’, ‘C1.0e+05_1.0e+06_02.50_07_00_2’, ‘C1.0e+05_1.0e+06_02.50_14_00_1’ ... ]]
#>
#> a1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> b1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> z1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> zpH1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> c1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> y1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>
#> a1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> b1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> z1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> zpH1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> c1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> y1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>
#> a1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> b1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> z1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> zpH1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> c1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> y1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>
#> a1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> b1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> z1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> zpH1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> c1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> y1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>
#> a1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> b1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> z1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> zpH1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> c1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> y1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>
#> a1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> b1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> z1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> zpH1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> c1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> y1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>
#> a1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> b1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> z1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> zpH1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> c1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> y1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>
#> a1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> b1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> z1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> zpH1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> c1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> y1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>
#> a1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> b1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> z1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> zpH1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> c1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> y1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>
#> a1 . . . . . . . . . . . . . . . . . .
#> b1 . . . . . . . . . . . . . . . . . .
#> z1 . . . . . . . . . . . . . . . . . .
#> zpH1 . . . . . . . . . . . . . . . . . .
#> c1 . . . . . . . . . . . . . . . . . .
#> y1 . . . . . . . . . . . . . . . . . .
# Accessing colData
tds$Mz
#> numeric-Rle of length 351 with 1 run
#> Lengths: 351
#> Values : 1211.7
tds$FilterString
#> NULL
# Subsetting
# First 100 fragments
tds[1:100]
#> TopDownSet object (0.31 Mb)
#> - - - Protein data - - -
#> Amino acid sequence (153): GLSDGEWQQVLNVWGKVEADIAGHGQ...GAMTKALELFRNDIAAKYKELGFQG
#> Mass : 16964.96
#> Modifications (3): Carbamidomethyl, Acetyl, Met-loss
#> - - - Fragment data - - -
#> Number of theoretical fragments: 100
#> Theoretical fragment types (12): a, a*, b, b*, c, ..., x*, y, y*, z, z*
#> Theoretical mass range: [72.04;1142.51]
#> - - - Condition data - - -
#> Number of conditions: 222
#> Number of scans: 351
#> Condition variables (59): File, Scan, ..., Sample, MedianIonInjectionTimeMs
#> - - - Intensity data - - -
#> Size of array: 100x351 (3.30% != 0)
#> Number of matched fragments: 1157
#> Intensity range: [280.27;214724.06]
#> - - - Processing information - - -
#> [2018-01-30 11:39:16] 14518 fragments [1949;351] matched (tolerance: 25 ppm, strategies ion/fragment: remove/remove).
#> [2018-01-30 11:39:16] Condition names updated based on: Mz, AgcTarget, EtdReagentTarget, EtdActivation, CidActivation, HcdActivation. Order of conditions changed. 222 conditions.
#> [2018-01-30 11:39:16] Recalculate median injection time based on: Mz, AgcTarget.
#> [2021-07-27 21:29:41] Subsetted 14518 fragments [1949;351] to 1157 fragments [100;351].
# All c fragments
tds["c"]
#> TopDownSet object (0.31 Mb)
#> - - - Protein data - - -
#> Amino acid sequence (153): GLSDGEWQQVLNVWGKVEADIAGHGQ...GAMTKALELFRNDIAAKYKELGFQG
#> Mass : 16964.96
#> Modifications (3): Carbamidomethyl, Acetyl, Met-loss
#> - - - Fragment data - - -
#> Number of theoretical fragments: 152
#> Theoretical fragment types (1): c
#> Theoretical mass range: [117.07;16925.98]
#> - - - Condition data - - -
#> Number of conditions: 222
#> Number of scans: 351
#> Condition variables (59): File, Scan, ..., Sample, MedianIonInjectionTimeMs
#> - - - Intensity data - - -
#> Size of array: 152x351 (0.63% != 0)
#> Number of matched fragments: 338
#> Intensity range: [432.91;664294.75]
#> - - - Processing information - - -
#> [2018-01-30 11:39:16] 14518 fragments [1949;351] matched (tolerance: 25 ppm, strategies ion/fragment: remove/remove).
#> [2018-01-30 11:39:16] Condition names updated based on: Mz, AgcTarget, EtdReagentTarget, EtdActivation, CidActivation, HcdActivation. Order of conditions changed. 222 conditions.
#> [2018-01-30 11:39:16] Recalculate median injection time based on: Mz, AgcTarget.
#> [2021-07-27 21:29:41] Subsetted 14518 fragments [1949;351] to 338 fragments [152;351].
# Just c 152
tds["c152"]
#> TopDownSet object (0.28 Mb)
#> - - - Protein data - - -
#> Amino acid sequence (153): GLSDGEWQQVLNVWGKVEADIAGHGQ...GAMTKALELFRNDIAAKYKELGFQG
#> Mass : 16964.96
#> Modifications (3): Carbamidomethyl, Acetyl, Met-loss
#> - - - Fragment data - - -
#> Number of theoretical fragments: 1
#> Theoretical fragment types (1): c
#> Theoretical mass range: [16925.98;16925.98]
#> - - - Condition data - - -
#> Number of conditions: 222
#> Number of scans: 351
#> Condition variables (59): File, Scan, ..., Sample, MedianIonInjectionTimeMs
#> - - - Intensity data - - -
#> Size of array: 1x351 (33.90% != 0)
#> Number of matched fragments: 119
#> Intensity range: [979.57;664294.75]
#> - - - Processing information - - -
#> [2018-01-30 11:39:16] 14518 fragments [1949;351] matched (tolerance: 25 ppm, strategies ion/fragment: remove/remove).
#> [2018-01-30 11:39:16] Condition names updated based on: Mz, AgcTarget, EtdReagentTarget, EtdActivation, CidActivation, HcdActivation. Order of conditions changed. 222 conditions.
#> [2018-01-30 11:39:16] Recalculate median injection time based on: Mz, AgcTarget.
#> [2021-07-27 21:29:41] Subsetted 14518 fragments [1949;351] to 119 fragments [1;351].
# Condition 1 to 10
tds[, 1:10]
#> TopDownSet object (0.35 Mb)
#> - - - Protein data - - -
#> Amino acid sequence (153): GLSDGEWQQVLNVWGKVEADIAGHGQ...GAMTKALELFRNDIAAKYKELGFQG
#> Mass : 16964.96
#> Modifications (3): Carbamidomethyl, Acetyl, Met-loss
#> - - - Fragment data - - -
#> Number of theoretical fragments: 1949
#> Theoretical fragment types (12): a, a*, b, b*, c, ..., x*, y, y*, z, z*
#> Theoretical mass range: [72.04;16925.98]
#> - - - Condition data - - -
#> Number of conditions: 6
#> Number of scans: 10
#> Condition variables (59): File, Scan, ..., Sample, MedianIonInjectionTimeMs
#> - - - Intensity data - - -
#> Size of array: 1949x10 (2.69% != 0)
#> Number of matched fragments: 524
#> Intensity range: [1843.09;669750.88]
#> - - - Processing information - - -
#> [2018-01-30 11:39:16] 14518 fragments [1949;351] matched (tolerance: 25 ppm, strategies ion/fragment: remove/remove).
#> [2018-01-30 11:39:16] Condition names updated based on: Mz, AgcTarget, EtdReagentTarget, EtdActivation, CidActivation, HcdActivation. Order of conditions changed. 222 conditions.
#> [2018-01-30 11:39:16] Recalculate median injection time based on: Mz, AgcTarget.
#> [2021-07-27 21:29:41] Subsetted 14518 fragments [1949;351] to 524 fragments [1949;10].