PlotSetArray-class {seqplots} | R Documentation

## PlotSetArray Reference Class

### Description

PlotSetArray Reference Class

### Fields

`data`

  a nested list holding the data

`annotations`

  list of annotations

### Methods

`anno(n)`

  Extracts the genomic locations for nth feature as GRanges

`as.array(x, ...)`

  Converts PlotSetArray calss to matrix of PlotSeqPairs

`get(i, j)`

  Subseting method, returns PlotSetArray

`getByID(i)`

  Subseting method, returns PlotSeqList

`getPairs(i)`

  Subseting method, takes pair IDs list, returns PlotSetList

`getRow(i)`

  Subseting method, get row of data as list

`info()`

  Outputs data.frame describing the content of PlotSetList

`nfeatures()`

  Outputs the number of features in the PlotSetArray

`ntracks()`

  Outputs the number of tracks in the PlotSetArray

`pairind()`

  Outputs the list of pair IDs

`plot(...)`

  Plot the PlotSetArray, i.e. all PlotSetPairs within class. See `plot` for datails.

`subset(i, j)`

  Subseting method, get PlotSetPair as list

`unlist()`

  Flattens PlotSetArray to PlotSetList

### Subsetting

`x` is an object of `PlotSetArray` class:

- `x[1:2,1:2]` produces `PlotSetArray` with 2 feature(s) and 2 tracks.

- `x[1:2]` produces `PlotSetList` with 2 feature/tracks pairs.

- `x[[1]]` produces single `PlotSetPair`.

- `unlist(x)` produces `PlotSetList` with all feature/tracks pairs.

- `x$as.array()` produces the matrix of `PlotSetPair` classes with all feature/tracks pairs.

### See Also

Other classes: `MotifSetup-class`, `PlotSetList-class`, `PlotSetPair-class`

[Package seqplots version 1.22.2 Index]