psubAxt {CNEr} | R Documentation

## Parallel subset of Axt alignment

### 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)

[Package CNEr version 1.22.0 Index]