RVD strings, one per TALE array

Renders each array as a separated string of its RVDs in part order — the form target-prediction tools consume.

Usage

tales_rvd_strings(x, sep = "-", repeats_only = TRUE)

Arguments

x

A tales object carrying an rvd column.

sep

Separator between RVDs. Defaults to "-", the convention used by AnnoTALE and by this package's own sample files.

repeats_only

Drop the terminus parts, whose rvd holds an anchor code rather than a real RVD (see tales_anchor_codes). TRUE by default, since target prediction concerns the central repeat domain only.

Value

A BStringSet, named by array_id.

See also

tales_coded_strings

Other tales projections: tales_coded_strings(), tales_domain_codes(), tales_get_dna_seq(), tales_get_protein_seq(), tales_to_universalmotif()

Examples

x <- tales_from_telltales(system.file("extdata", "tellTaleExampleOutput",
                                      package = "tantale"))
tales_rvd_strings(x)[1]
#> BStringSet object of length 1:
#>     width seq                                               names               
#> [1]    77 NN-NG-NN-HD-HD-NI-N*-NG...NG-HD-NI-NI-NG-HD-NN-NG ROI_00001
tales_rvd_strings(x, repeats_only = FALSE)[1] # keeps NTERM/CTERM markers
#> BStringSet object of length 1:
#>     width seq                                               names               
#> [1]    89 NTERM-NN-NG-NN-HD-HD-NI...NI-NI-NG-HD-NN-NG-CTERM ROI_00001