PlotSetArray-class: PlotSetArray Reference Class

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

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

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