MotifSetup-class {seqplots} | R Documentation

## MotifSetup Reference Class

### Description

This class is used to initialize motif plots and mix them with track plots.

### Details

Usage note - the `addMotif` and `addBigWig` methods can be chained in following way: `MotifSetup()$addMotif("GAGA", window=200L)$addBigWig("path/to/file.bw")`

### Fields

`data`

  a nested list holding the data

`annotations`

  list of annotations

### Methods

`addBigWig(file_path)`

  Adds new BigWig file.

`addMotif(pattern, window = 200L, heatmap = TRUE, revcomp = TRUE, genome = NULL, name = pattern)`

  Adds new motif.

`nmotifs()`

  Prints number of motifs in class

### See Also

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

### Examples

    #Motifs only
    motif1 <- MotifSetup()
    motif1$addMotif("GAGA", window=200L)
    motif1$addMotif("TATA", window=100L, name="TATA box")

    #Motifs and BigWigs
    motif2 <- MotifSetup()
    motif2$addMotif("GAGA", window=200L)
    motif2$addBigWig("path/to/file.bw")

    #Chaining commands
    motif3 <- MotifSetup()$addMotif("GAGA")$addBigWig("path/to/file.bw")

[Package seqplots version 1.22.2 Index]