MotifSetup-class: MotifSetup Reference Class

Description Details Fields Methods See Also Examples

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

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#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")
 

Przemol/seqplots documentation built on July 7, 2019, 10:26 p.m.