fixCoordinates: Fix the coordinates in 'Axt' object

Description Usage Arguments Details Value Author(s) Examples

Description

In ‘axt’ file and Axt object, the coordinates of negative query alignments are relative to the reverse-complemented coordinates of its chromosome. This is different from the convention in Bioconductor. This function fixes the coordinates which are always relative to the positive strand.

Usage

1

Arguments

x

Axt object.

Details

In Axt, the ‘strand’ is for the aligning organism. If the strand value is “-”, the values of the aligning organism's start and end fields are relative to the reverse-complemented coordinates of its chromosome.

Value

A Axt object.

Author(s)

Ge Tan

Examples

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  axtFnDanRer10Hg38 <- file.path(system.file("extdata", package="CNEr"),
                                 "danRer10.hg38.net.axt")
  qAssemblyFn <- file.path(system.file("extdata",
                                       package="BSgenome.Hsapiens.UCSC.hg38"),
                           "single_sequences.2bit")
  tAssemblyFn <- file.path(system.file("extdata",
                                       package="BSgenome.Drerio.UCSC.danRer10"),
                           "single_sequences.2bit")
  axtDanRer10Hg38 <- readAxt(axtFnDanRer10Hg38, tAssemblyFn=tAssemblyFn,
                             qAssemblyFn=qAssemblyFn)
  ## Fix the coordinates
  fixCoordinates(axtDanRer10Hg38)
  
  ## Restore it
  fixCoordinates(fixCoordinates(axtDanRer10Hg38))

CNEr documentation built on May 20, 2017, 9:22 p.m.

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