Support RleList genomic tracks for compartment eigenvector phasing

[Copilot]

getCompartments() already supported phasing with sequence/gene-derived inputs, but not with coverage-style genomic tracks. This PR adds support for BigWig-imported tracks provided as RleList, so compartment sign phasing can use arbitrary per-base signal tracks (e.g. GC coverage tracks).

• Core fix: RleList phasing path

  • In .eigChr(), the RleList branch now correctly uses the provided track as the coverage source before computing per-bin means.
  • This resolves the broken code path where the coverage object was referenced but never initialized.

• API/docs alignment

  • Updated getCompartments() parameter docs to explicitly list supported genome input types: BSgenome, DNAStringSet, TxDb, and RleList.
  • Synced generated Rd docs with the updated contract.

• Focused test coverage

  • Added a test that builds an RleList track and runs:
    • getCompartments(full_contacts_yeast, genome = cov_track, chromosomes = "VI")
  • Verifies the RleList phasing route executes without error for a chromosome-scoped run.

cov_track <- IRanges::RleList(
  VI = IRanges::Rle(seq_len(max(GenomicRanges::end(VI_regions))))
)

comps <- getCompartments(
  full_contacts_yeast,
  genome = cov_track,
  chromosomes = "VI"
)

[js2264]

In the test for phasing with coverage track, use a coverage track of GC content (calculated from the yeast genomic sequence, and smoothed along chromosomes with a bon width of 100)

[js2264]

@copilot In the test for phasing with coverage track, use a coverage track of GC content (calculated from the yeast genomic sequence, and smoothed along chromosomes with a bon width of 100). Also, IRanges::Rle() does not exist

[Copilot]

Addressed in commit cfe7482 (plus cleanup 06a8417): the test now uses GC-content coverage from yeast sequence with 100-bin smoothing, and replaces IRanges::Rle() with S4Vectors::Rle() inside an IRanges::RleList.

[Copilot]

In the test for phasing with coverage track, use a coverage track of GC content (calculated from the yeast genomic sequence, and smoothed along chromosomes with a bon width of 100)

Updated in commit cfe7482 (plus follow-up cleanup 06a8417): the test now builds an RleList GC-coverage track from the yeast reference genome and smooths it along chromosomes with bin width 100 before calling getCompartments().