Changes in version 0.99.9                        

CHANGES

  - Authors@R lists the funders (ERA-NET Transcan-Neu III - EPILUNAR,
    grant 01KT2409; Saarland University NanoBioMed Young Investigator
    Grant) with the fnd role.
  - inst/CITATION rewritten: the citation reads "Gunduz IB, Murugan SK,
    Mueller F (year). methylTFR: ... R package version x.y.z.", takes
    the version and year from DESCRIPTION, and carries the Bioconductor
    DOI.
  - The README shows the citation and BibTeX entry.
  - Added CITATION.cff (excluded from the build via .Rbuildignore).

BUG FIXES

  - rnb_sample_ids() no longer calls RnBeads::samples(), which is not
    exported by all RnBeads versions (R CMD check: "Missing or
    unexported object"). Sample identifiers are read from the
    identifiers.column of RnBeads::pheno(), with the previous fallbacks
    unchanged.
  - The vignette, README and inst/scripts/vignette_data.R call
    getGenomeGC() without an argument, which works with every version of
    the annotation packages.

                       Changes in version 0.99.8                        

BUG FIXES

  - read_methylome(type = "encode") returned methylation scores that
    were not fractions. parse_encode() divided column 11 by column 10,
    but in a bedMethyl file column 10 is read coverage and column 11 is
    the percentage of reads methylated, so a fully methylated CpG
    covered by five reads scored 20. The score is now the percentage
    over 100.
  - parse_encode() skipped the first line of every file unconditionally.
    Files downloaded from ENCODE carry no header, so the first record
    was silently discarded. The header is now detected.
  - read_methylome() stops if the parsed scores fall outside 0 to 1
    rather than passing them to the deviation calculation.
  - The run_methylTFR_RnBeads() example built an RnBiseqSet without
    setting identifiers.column, so samples() returned row numbers and
    the example stopped on the sample-identifier check. It now sets the
    option before building the set and restores it afterwards.
  - The bundled encode.tsv.gz example has been rebuilt. Columns 10
    and 11 are now named coverage and percentMeth rather than blockCount
    and blockSizes, and the percentages span 0 to 100, so the tests
    exercise the case the old example passed by luck.

                       Changes in version 0.99.7                        

NEW FEATURES

  - Added run_methylTFR_RnBeads(), which runs the methylTFR workflow
    directly on a preprocessed RnBeads object instead of per-sample BED
    files. Samples are read one column at a time, so disk-backed RnBeads
    sets are never loaded into memory in full.
  - Added computeZScoreVariability(), which ranks TF motifs by how much
    their activity varies across samples and tests each motif against a
    chi-squared null. Deviation scores are first calibrated against a
    within-sample null estimated across motifs, so that a variability
    above 1 is interpretable as "more variable than background".
  - methylTFRdeviations objects returned by run_methyltfr() and
    run_methylTFR_RnBeads() now carry a third assay, expected, holding
    the GC-derived expected deviations. These were previously computed
    and then discarded.

BUG FIXES

  - run_methyltfr() no longer rejects .csv sample annotation files. The
    .tsv branch's else clause caught every .csv file and raised an error
    after the file had already been read.
  - differential_deviation_test() now falls back to colnames(deviations)
    when groups is NULL, instead of colnames(groups), which was always
    NULL. Group labels are also validated against the number of columns.
  - The invalid-input fallback for cov_threshold in run_methyltfr() now
    sets the documented default of 1 rather than 5.

DOCUMENTATION

  - The heatmap in the memory T cell vignette is now drawn with
    ComplexHeatmap instead of ggplot2, with columns split by cell type
    and rows clustered.
  - The compartment-agreement scatter plot in the same vignette now
    colours each motif by where it is differential: red for both
    compartments, green for CD4 only, blue for CD8 only and grey for
    neither.

INTERNAL

  - The per-sample deviation loop shared by both entry points was
    factored out into methyltfr_core(), so the file-based and
    RnBeads-based workflows are guaranteed to produce identical results
    for the same methylation calls.

                       Changes in version 0.99.0                        

NEW FEATURES

  - Added a NEWS.md file to track changes to the package.