anchorlift: anchorlift

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

anchorlift

Description

"lifts" all queries with respect to subject in coordinates that are within "pad" i.e. puts the queries into subject-centric coordinates, which is a new genome with label "Anchor" (default)

Respects strand of subject (i.e. if subject strand gr is "-" then will lift all queries to the left of it into positive subject-centric coordinates). Keeps track of subject and query id for later deconvolution if need be.

Usage

anchorlift(
  query,
  subject,
  window = 1e+09,
  by = NULL,
  seqname = "Anchor",
  include.values = TRUE,
  verbose = TRUE,
  ...
)

Arguments

query	GRanges that will be lifted around the subject
subject	GRanges around which the queries will be lifted
window	integer specifying how far around each subject to gather query intervals to lift (default = 1e9)
by	character vector specifying additional columms (e.g. sample id) around which to restrict overlaps (via gr.findoverlaps()). Refer to 'gr.findoverlaps()' documentation. (default = NULL)
seqname	String specifying the name of the output sequence around which to anchor (default = "Anchor")
include.values	Boolean Flag whether to include values from query and subject (default = TRUE)

Value

anchorlifted GRanges

Author(s)

Marcin Imielinski

mskilab/gUtils documentation built on June 6, 2023, 12:08 a.m.