seqplots-generic: SeqPlots generic methods

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

Description

Generic operators working with PlotSetArray, PlotSetList and PlotSetPair to subset or flatten the data structure.

Usage

## S4 method for signature 'PlotSetList,ANY,ANY,ANY'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'PlotSetList,ANY,ANY'
x[[i, j, ...]]

## S4 method for signature 'PlotSetArray,ANY,missing,ANY'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'PlotSetArray,ANY,vector,ANY'
x[i, j]

## S4 method for signature 'PlotSetArray,ANY,ANY'
x[[i, j, ...]]

Arguments

x	an object of class PlotSetArray, PlotSetList or PlotSetPair
i	indices specifying elements to extract or replace. Indices are numeric or character vectors or empty (missing) or NULL. Numeric values are coerced to integer as by as.integer (and hence truncated towards zero). Character vectors will be matched to the names of the object (or for matrices/arrays, the dimnames): see ‘Character indices’ below for further details. For [-indexing only: i, j, ... can be logical vectors, indicating elements/slices to select. Such vectors are recycled if necessary to match the corresponding extent. i, j, ... can also be negative integers, indicating elements/slices to leave out of the selection. When indexing arrays by [ a single argument i can be a matrix with as many columns as there are dimensions of x; the result is then a vector with elements corresponding to the sets of indices in each row of i. An index value of NULL is treated as if it were integer(0).
j	see description for i
...	see description for i
drop	For matrices and arrays. If TRUE the result is coerced to the lowest possible dimension (see the examples). This only works for extracting elements, not for the replacement. See drop for further details.

Value

If x is 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.

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

If x is PlotSetList class:

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

• x[[1]] produces single PlotSetPair.

See Also

Extract

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