expand: expand

In mskilab/gChain: R Package Providing Additional Capabilities and Speed for GenomicRanges Operations

expand

Description

GChain::expand

Expands gChain by "space" base pairs. By default will pad the x intervals with space and pad and shift the y intervals, however this can be changed with the shift.x and shift.y flags.

This is useful when gChain represents a multiple sequence alignment, and we would like to visualize data lifted "around" the alignment, e.g. some window upwards or downwards

If abs(scale) of the gChain != 1, then space will be added to the "smaller" space and space*scale positions will be added to the larger space, i.e. if abs(scale)<1 then y is the smaller space, if abs(scale)>1, then x is the smaller space

if space = Inf, then the Chain will map the entire sequence length (ie the whole chromosome) (of x or y, whichever is the largest for the given interval pair)

Usage

## S4 method for signature 'gChain'
expand(x, space = NULL, shift.x = FALSE, shift.y = TRUE)

mskilab/gChain documentation built on Sept. 28, 2022, 3:45 p.m.