psubAxt: Parallel subset of Axt alignment

In CNEr: CNE Detection and Visualization

Description

Given two GRanges objects, select the Axt alignments whose the target and query alignments are both within each pair of ranges.

Usage

  psubAxt(x, targetSearch, querySearch)

Arguments

x	Axt object.
targetSearch,querySearch	GRanges objects: the ranges to keep for target and query alignments. They must be of the same length. Strand information is ignored.

Details

The ‘targetSearch’ and ‘querySearch’ have the coordinates relative to the positive strand. For each pair of the ranges, the alignments that lie within both the target and query range are kept.

Value

A Axt object.

Author(s)

Ge Tan

See Also

psubAxt

Examples

  library(GenomicRanges)
  tAssemblyFn <- file.path(system.file("extdata",
                             package="BSgenome.Drerio.UCSC.danRer10"),
                           "single_sequences.2bit")
  qAssemblyFn <- file.path(system.file("extdata",
                             package="BSgenome.Hsapiens.UCSC.hg38"),
                           "single_sequences.2bit")
  axtFn <- file.path(system.file("extdata", package="CNEr"), 
                     "danRer10.hg38.net.axt")
  axt <- readAxt(axtFn, tAssemblyFn, qAssemblyFn)

  targetSearch <- GRanges(seqnames=c("chr6"),
                          ranges=IRanges(start=c(24000000, 26900000),
                                         end=c(24060000, 26905000)),
                          strand="+"
                          )
  querySearch <- GRanges(seqnames=c("chr7", "chr2"),
                         ranges=IRanges(start=c(12577000, 241262700),
                                        end=c(12579000, 241268600)),
                         strand="+"
                         )
  psubAxt(axt, targetSearch, querySearch)

CNEr documentation built on Nov. 8, 2020, 5:36 p.m.