lift: lift

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

lift

Description

Takes GRanges input and returns GRanges output Output GRanges values() fields are tagged with the following values to allow mapping to input (1) query.id - index of query matching this GRanges (2) query.start - start of this GRanges in the query.id query (3) query.end - end of this GRanges in the query.id query (4) link.id - index of link in gChain used to make this mapping

Output GRanges will retain all other values features of the query gRanges that yielded it.

GRangesList can be also provided as input x, in which case the output will be a GRL or list of data frames one for each input

If x is a gTrack object, then output will be a gTrack object. gTrack inputs should be of length 1.

if split.grl = TRUE, grl outputs are split via grl.split according to (mapped) seqname and strand

Remaining args passed on to gr.findoverlaps

Usage

## S4 method for signature 'gChain'
lift(
  .Object,
  x,
  format = "GRanges",
  split.grl = FALSE,
  pintersect = NA,
  by = NULL,
  verbose = TRUE,
  ...
)

Arguments

x	GRanges to lift through this chain
format	INFO INFO
split.grl	flag whether or not to split output into GRangesList for GRangesList input

Author(s)

Marcin Imielinski

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