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Sliding window

Source: R/slidingWindow.R
slidingWindow.Rd

This function is used to subset a GBreaks object into a list of GBreaks using a sliding window.

Usage

slidingWindow(
  gb,
  factor = 100,
  windowSize = NULL,
  stepSize = NULL,
  merged = FALSE,
  cut = TRUE
)

Arguments

gb

A GBreaks object.

windowSize

The size of the window.

stepSize

The size of the step.

merged

set TRUE to output a 'GBreaks' object

cut

whether cut the alignments out of the window

type

slide the window on the reference genome or query genome (reference/query)

Value

Returns a list of GBreaks objects, one for each window.

See also

Other Similarity indexes: GOC(), JC69_distance(), K80_distance(), T92_distance(), correlation_index(), karyotype_index(), strand_randomisation_index(), synteny_index()

Author

Zhang Kun

Examples

exdata_Sac <- system.file("extdata/SacCer3__SacPar.gff3.gz", package = "GenomicBreaks")
gb <- load_genomic_breaks(exdata_Sac, BSgenome.Scerevisiae.UCSC.sacCer3::Scerevisiae)
slided_gb <- slidingWindow(gb, windowSize = 1e5, stepSize = 5e4)
#> Warning: The 2 combined objects have no sequence levels in common. (Use
#>   suppressWarnings() to suppress this warning.)
#> Warning: The 2 combined objects have no sequence levels in common. (Use
#>   suppressWarnings() to suppress this warning.)
#> Warning: The 2 combined objects have no sequence levels in common. (Use
#>   suppressWarnings() to suppress this warning.)
#> Warning: The 2 combined objects have no sequence levels in common. (Use
#>   suppressWarnings() to suppress this warning.)
#> Warning: The 2 combined objects have no sequence levels in common. (Use
#>   suppressWarnings() to suppress this warning.)
#> Warning: The 2 combined objects have no sequence levels in common. (Use
#>   suppressWarnings() to suppress this warning.)
#> Warning: The 2 combined objects have no sequence levels in common. (Use
#>   suppressWarnings() to suppress this warning.)
#> Warning: The 2 combined objects have no sequence levels in common. (Use
#>   suppressWarnings() to suppress this warning.)
#> Warning: The 2 combined objects have no sequence levels in common. (Use
#>   suppressWarnings() to suppress this warning.)
#> Warning: The 2 combined objects have no sequence levels in common. (Use
#>   suppressWarnings() to suppress this warning.)
#> Warning: The 2 combined objects have no sequence levels in common. (Use
#>   suppressWarnings() to suppress this warning.)
#> Warning: The 2 combined objects have no sequence levels in common. (Use
#>   suppressWarnings() to suppress this warning.)
#> Warning: The 2 combined objects have no sequence levels in common. (Use
#>   suppressWarnings() to suppress this warning.)
#> Warning: The 2 combined objects have no sequence levels in common. (Use
#>   suppressWarnings() to suppress this warning.)
#> Warning: The 2 combined objects have no sequence levels in common. (Use
#>   suppressWarnings() to suppress this warning.)
#> Warning: The 2 combined objects have no sequence levels in common. (Use
#>   suppressWarnings() to suppress this warning.)
slided_gb[[1]]
#> GBreaks object with 6 ranges and 6 metadata columns:
#>       seqnames       ranges strand |     score                    query
#>          <Rle>    <IRanges>  <Rle> | <numeric>                <GRanges>
#>   [1]     chrI   5860-10010      + |     10609   NC_047487.1:8723-12716
#>   [2]     chrI  11157-11782      + |      1253  NC_047487.1:13035-13680
#>   [3]     chrI  25371-26528      + |      3651  NC_047487.1:15380-16537
#>   [4]     chrI  26849-29699      + |      6130  NC_047487.1:17263-20175
#>   [5]     chrI  29937-30607      + |       767  NC_047487.1:20203-20866
#>   [6]     chrI 31155-100000      + |    298623 NC_047487.1:21379-128635
#>       window_id window_seqname window_start window_end
#>       <integer>    <character>    <integer>  <integer>
#>   [1]         1           chrI            1     100000
#>   [2]         1           chrI            1     100000
#>   [3]         1           chrI            1     100000
#>   [4]         1           chrI            1     100000
#>   [5]         1           chrI            1     100000
#>   [6]         1           chrI            1     100000
#>   -------
#>   seqinfo: 17 sequences (1 circular) from sacCer3 genome