Construct a GBreaks object from a permutation vector

Inverse of permutationVector(): builds a GBreaks object of evenly spaced blocks from a signed permutation.

Usage

permutationVectorToGBreaks(
  v,
  tsplit = length(v),
  qsplit = length(v),
  width = 90,
  spacing = 100
)

Arguments

v

A signed permutation of 1:n, as returned by permutationVector().

tsplit, qsplit

Number of blocks in each sequence of the target and query genomes, in order. They must sum to n.

width

Width of the blocks.

spacing

Distance between the starts of consecutive blocks.

Value

A GBreaks object of length n, sorted, such that permutationVector() returns v.

Details

Block i of the target genome is aligned to position abs(v[i]) of the query genome, on the minus strand if v[i] is negative. The blocks are placed every spacing bases on each genome, starting at position spacing, and the genomes are cut into sequences of tsplit and qsplit blocks, named chrT1, chrT2, etc. and chrQ1, chrQ2, etc. Sequence lengths are set, so that the object can be passed to reverse().

See also

simulateRearrangements()

Examples

# The double inversion of exampleDoubleInversion1
permutationVector(exampleDoubleInversion1)
#> [1]  1  4 -2 -3  5
permutationVectorToGBreaks(c(1, 4, -2, -3, 5))
#> GBreaks object with 5 ranges and 1 metadata column:
#>       seqnames    ranges strand |         query
#>          <Rle> <IRanges>  <Rle> |     <GRanges>
#>   [1]    chrT1   100-189      + | chrQ1:100-189
#>   [2]    chrT1   200-289      + | chrQ1:400-489
#>   [3]    chrT1   300-389      - | chrQ1:200-289
#>   [4]    chrT1   400-489      - | chrQ1:300-389
#>   [5]    chrT1   500-589      + | chrQ1:500-589
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome
permutationVectorToGBreaks(c(1, 4, -2, -3, 5)) |> flagDoubleInversions()
#> GBreaks object with 5 ranges and 2 metadata columns:
#>       seqnames    ranges strand |         query       Dbl
#>          <Rle> <IRanges>  <Rle> |     <GRanges> <logical>
#>   [1]    chrT1   100-189      + | chrQ1:100-189      TRUE
#>   [2]    chrT1   200-289      + | chrQ1:400-489     FALSE
#>   [3]    chrT1   300-389      - | chrQ1:200-289     FALSE
#>   [4]    chrT1   400-489      - | chrQ1:300-389     FALSE
#>   [5]    chrT1   500-589      + | chrQ1:500-589     FALSE
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome

# On two target sequences
permutationVectorToGBreaks(c(1, 4, -2, -3, 5), tsplit = c(2, 3))
#> GBreaks object with 5 ranges and 1 metadata column:
#>       seqnames    ranges strand |         query
#>          <Rle> <IRanges>  <Rle> |     <GRanges>
#>   [1]    chrT1   100-189      + | chrQ1:100-189
#>   [2]    chrT1   200-289      + | chrQ1:400-489
#>   [3]    chrT2   100-189      - | chrQ1:200-289
#>   [4]    chrT2   200-289      - | chrQ1:300-389
#>   [5]    chrT2   300-389      + | chrQ1:500-589
#>   -------
#>   seqinfo: 2 sequences from an unspecified genome