Axt-class {CNEr} | R Documentation

## Class `"Axt"`

### Description

The Axt S4 object to hold a axt file.

### Usage

    ## Constructors:
    Axt(targetRanges=GRanges(), targetSeqs=DNAStringSet(),
        queryRanges=GRanges(), querySeqs=DNAStringSet(),
        score=integer(0), symCount=integer(0), names=NULL)

    ## Accessor-like methods:
    ## S4 method for signature 'Axt'
    targetRanges(x)
    ## S4 method for signature 'Axt'
    targetSeqs(x)
    ## S4 method for signature 'Axt'
    queryRanges(x)
    ## S4 method for signature 'Axt'
    querySeqs(x)
    ## S4 method for signature 'Axt'
    score(x)
    ## S4 method for signature 'Axt'
    symCount(x)
    ## ... and more (see Methods)

### Arguments

`targetRanges` | Object of class `"GRanges"`: The ranges of net alignments on reference genome.
`targetSeqs` | Object of class `"DNAStringSet"`: The alignment sequences of reference genome.
`queryRanges` | Object of class `"GRanges"`: The ranges of net alignments on query genome.
`querySeqs` | Object of class `"DNAStringSet"`: The alignment sequences of query genome.
`score` | Object of class `"integer"`: The alignment score.
`symCount` | Object of class `"integer"`: The alignment length.
`names` | `character`(): the names of axt alignments.
`x` | Object of class `"Axt"`: A Axt object.

### Details

In ‘axt’ files and `Axt` object, the ‘targetRanges’ also have the alignments on positive strands. However, the ‘queryRanges’ can have alignments on negative strands, and the coordinates are based on negative strands, which is quite different from the convention in Bioconductor. To convert the coordinates of alignments on the negative strand to the positive strand, use `normaliseStrand`.

### Methods

[

  `signature(x = "Axt", i = "ANY", j = "ANY")`: Axt getter

c

  `signature(x = "Axt")`: Axt concatenator.

length

  `signature(x = "Axt")`: Get the number of alignments.

queryRanges

  `signature(x = "Axt")`: Get the ranges of query genome.

querySeqs

  `signature(x = "Axt")`: Get the alignment sequences of query genome.

score

  `signature(x = "Axt")`: Get the alignment score.

symCount

  `signature(x = "Axt")`: Get the alignment lengths.

targetRanges

  `signature(x = "Axt")`: Get the ranges of reference genome.

targetSeqs

  `signature(x = "Axt")`: Get the alignment sequences of reference genome.

### Author(s)

Ge Tan

### See Also

`readAxt` `writeAxt` `subAxt` `fixCoordinates` `makeAxtTracks`

### Examples

      library(GenomicRanges)
      library(Biostrings)
      ## Constructor
      targetRanges <- GRanges(seqnames=c("chr1", "chr1", "chr2", "chr3"),
                              ranges=IRanges(start=c(1, 20, 2, 3),
                                             end=c(10, 25, 10, 10)),
                              strand="+")
      targetSeqs <- DNAStringSet(c("ATTTTATGTG", "GGGAAG", "GGGCTTTTG",
                                   "TTGTGTAG"))
      queryRanges <- GRanges(seqnames=c("chr1", "chr10", "chr10", "chr20"),
                             ranges=IRanges(start=c(1, 25, 50, 5),
                                            end=c(10, 30, 58, 12)),
                             strand="+")
      querySeqs <- DNAStringSet(c("ATTTAAAGTG", "GGAAAA", "GGGCTCTGG",
                                  "TTAAATAA"))
      score <- c(246L, 4422L, 5679L, 1743L)
      symCount <- c(10L, 6L, 9L, 8L)
      axt <- Axt(targetRanges=targetRanges, targetSeqs=targetSeqs,
                 queryRanges=queryRanges, querySeqs=querySeqs,
                 score=score, symCount=symCount)

      ## getters
      names(axt)
      length(axt)
      first(axt)
      last(axt)
      seqnames(axt)
      strand(axt)
      seqinfo(axt)

      ## Vector methods
      axt[1]

      ## List methods
      unlist(axt)

      ## Combining
      c(axt, axt)

[Package CNEr version 1.20.0 Index]