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Load pairwise genome alignments

Source: R/load_genomic_breaks.R
load_genomic_breaks.Rd

Loads alignments of a query genome to a target genome from a text file in General Feature Format 3 (GFF3) or Multiple Alignemnt Format (MAF). By convention, the target genome is the one that was indexed by the aligner.

Usage

load_genomic_breaks(
  file,
  target_bsgenome = NULL,
  query_bsgenome = NULL,
  sort = TRUE,
  type = "match_part"
)

Arguments

file

Path to a file in GFF3 or MAF format. The file can be compressed with gzip.

target_bsgenome

A BSgenome object or path to a FASTA file representing the target genome.

query_bsgenome

A BSgenome object or path to a FASTA file representing the query genome.

sort

Returns the object sorted, ignoring strand information.

type

In GFF3 files, Sequence Ontology term representing an alignment block (default: match_part).

Value

Returns a GBreaks object where each element represents a pairwise alignment block. The granges part of the object contains the coordinates on the target genome, and the query metadata column contains the query coordinates in GRanges format. The seqinfo of each BSgenome object passed as parameters are copied to the GRanges objects accordingly.

Details

When the input is in GFF3 files, this function expects the pairwise alignment to be represented in in the following way:

  • Alignments blocks are represented by entries in specific sequence ontology term in the type column. Other entries will be discarded. The default type is match_part.

  • The coordinate system of the file is the one of the target genome.

  • The Target tag in the attribute column contains the coordinates of the match in the query genome. (Sorry that it is confusing…)

  • Stand information is set so that query genome coordinates are always on the plus strand.

See also

The MAF format documentation on the UCSC genome browser website, and the GFF3 specification from the Sequence Ontology group.

Examples

load_genomic_breaks(system.file("extdata/contigs.genome.maf.gz", package = "GenomicBreaks"))
#> GBreaks object with 2 ranges and 4 metadata columns:
#>         seqnames     ranges strand |     score
#>            <Rle>  <IRanges>  <Rle> | <integer>
#>   [1] MT192765.1    25-8666      + |     52990
#>   [2] MT192765.1 8882-29829      - |    128566
#>                                             query   aLength   matches
#>                                         <GRanges> <integer> <integer>
#>   [1]    NODE_2_length_8774_cov_178.827802:6-8647      8642      8642
#>   [2] NODE_1_length_20973_cov_191.628754:26-20973     20948     20945
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome

if (FALSE) { # \dontrun{
library("BSgenome.Scerevisiae.UCSC.sacCer3")
load_genomic_breaks(
  system.file("extdata/SacCer3__SacPar.gff3.gz", package = "GenomicBreaks"),
  target = Scerevisiae,
  query = NULL)
} # }