MotifSetup-class: MotifSetup Reference Class

In seqplots: An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps

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")
 

seqplots documentation built on Nov. 8, 2020, 4:52 p.m.