NCBSet-class {topdownr} | R Documentation

## The NCBSet class

### Description

The NCBSet class is a container for a top-down proteomics experiment similar to the TopDownSet but instead of intensity values it just stores the information if a bond is covered by a N-terminal (encoded as `1`), a C-terminal (encoded as `2`) and/or bidirectional fragments (encoded as `3`).

### Usage

    ## S4 method for signature 'NCBSet'
    bestConditions(
      object,
      n = ncol(object),
      minN = 0L,
      maximise = c("fragments", "bonds"),
      ...
    )

    ## S4 method for signature 'NCBSet'
    fragmentationMap(
      object,
      nCombinations = 10,
      cumCoverage = TRUE,
      maximise = c("fragments", "bonds"),
      labels = colnames(object),
      alphaIntensity = TRUE,
      ...
    )

    ## S4 method for signature 'NCBSet'
    show(object)

    ## S4 method for signature 'NCBSet'
    summary(object, what = c("conditions", "bonds"), ...)

### Arguments

`object` | `NCBSet`
`n` | `integer`, max number of combinations/iterations.
`minN` | `integer`, stop if there are less than `minN` additional fragments
`maximise` | `character`, optimisation targeting for the highest number of `"fragments"` (default) or `"bonds"`.
`nCombinations` | `integer`, number of combinations to show (0 to avoid plotting them at all).
`cumCoverage` | `logical`, if `TRUE` (default) cumulative coverage of combinations is shown.
`labels` | `character`, overwrite x-axis labels.
`alphaIntensity` | `logical`, if `TRUE` (default) the alpha level of the color is used to show the `colData(object)$AssignedIntensity`. If `FALSE` the alpha is set to `1`.
`what` | `character`, specifies whether `"conditions"` (columns; default) or `"bonds"` (rows) should be summarized.
`...` | arguments passed to internal/other methods. added.

### Value

An NCBSet object.

### Methods (by generic)

- `bestConditions`: Best combination of conditions.

  Finds the best combination of conditions for highest coverage of fragments or bonds. If there are two (or more conditions) that would add the same number of fragments/bonds the one with the highest assigned intensity is used. Use `n` to limit the number of iterations and combinations that should be returned. If `minN` is set at least `minN` fragments have to be added to the combinations. The function returns a 7-column matrix. The first column contains the index (`Index`) of the condition (column number). The next columns contain the newly added number of fragments or bonds (`FragmentsAddedToCombination`, `BondsAddedToCombination`), the fragments or bonds in the condition (`FragmentsInCondition`, `BondsInCondition`), and the cumulative coverage fragments or bonds (`FragmentCoverage`, `BondCoverage`).

- `fragmentationMap`: Plot fragmentation map.

  Plots a fragmentation map of the Protein. Use `nCombinations` to add another plot with `nCombinations` combined conditions. If `cumCoverage` is `TRUE` (default) these combinations increase the coverage cumulatively.

- `summary`: Summary statistics.

  Returns a `matrix` with some statistics: number of fragments, total/min/first quartile/median/mean/third quartile/maximum of intensity values.

### Slots

`rowViews`

  Biostrings::XStringViews, information about bonds (name, start, end, width, sequence), see Biostrings::XStringViews for details.

`colData`

  S4Vectors::DataFrame, information about the MS2 experiments and the fragmentation conditions.

`assay`

  Matrix::dgCMatrix, coverage values of the bonds. The rows correspond to the bonds and the columns to the condition/run. It just stores values that are different from zero. If a bond is covered by an N-terminal fragment its encoded with `1`, by an C-terminal fragmentl with `2` and by both fragment types/bidirectional by `3` respectively.

`files`

  `character`, files that were imported.

`processing`

  `character`, log messages.

### Author(s)

Sebastian Gibb mail@sebastiangibb.de

### See Also

- An `NCBSet` is generated from an TopDownSet object.

- Biostrings::XStringViews for the row view interface.

- Matrix::dgCMatrix for technical details about the coverage storage.

### Examples

    ## Example data
    data(tds, package="topdownr")

    ## Aggregate technical replicates
    tds <- aggregate(tds)

    ## Coercion into an NCBSet object
    ncb <- as(tds, "NCBSet")

    ncb

    head(summary(ncb))

    # Accessing slots
    rowViews(ncb)
    colData(ncb)
    head(assayData(ncb))

    # Accessing colData
    ncb$Mz

    # Subsetting

    # First 100 bonds
    ncb[1:100]

    # Just bond 152
    ncb["bond152"]

    # Condition 1 to 10
    ncb[, 1:10]

    # Plot fragmentation map
    fragmentationMap(ncb)

[Package topdownr version 1.10.0 Index]