adaptive_liftover: adaptive_liftover

In ThomasDCY/AdaLiftOver: Adaptive liftOver

adaptive_liftover

Description

Generate candidate target regions

Usage

adaptive_liftover(
  gr,
  chain,
  window = 2000L,
  option = "adaptive",
  gap = 5L,
  step_size = 200L,
  verbose = TRUE
)

Arguments

gr	The query regions of GRanges class.
chain	The chain object obtained from rtracklayer::import.chain().
window	The window size (bp) around the query regions. Default is 2000L.
option	The option for adaptive_liftover option = 'direct', apply direct liftOver to the query regions; option = 'local', apply local liftOver by extending the query regions by a window size; option = 'adaptive', apply direct liftOver first, for these failing to map, apply local liftOver.
gap	Ignore the gaps among target regions if below this value (bp). Default it 5L.
step_size	The step_size for generating candidate target regions. Default is 200L.
verbose	Print messages or not. Default is TRUE.

Value

The candidate target regions of GRangesList class with length equal to the query regions.

Author(s)

Chenyang Dong [e-mail]

Examples

## Not run: 
data('data_example')
## the reciprocal chain file can be downloaded from UCSC
chain <- import.chain('mm10.hg38.rbest.chain')
gr_target_list <- adaptive_liftover(gr, chain, window = 2000, step_size = 10000)
gr_target_list <- adaptive_liftover(gr, chain, window = 2000, step_size = 200)

## End(Not run)

ThomasDCY/AdaLiftOver documentation built on June 2, 2025, 12:35 p.m.