NEWS

---

EpiCompare 1.3.4

New features

• Example report:
  • Delete report/ folder and upload to Releases instead: https://github.com/neurogenomics/EpiCompare/releases
  • Add Rscript to replicate example report in inst/examples.
• EpiCompare
  • New arg add_download_button.
  • Always keep download button for post-processed peak files.
• `save_output``
  • Change .txt suffixes to more informative .csv suffixes for saved files.
• Create EpiArchives and offload report to there:
  • Updated vignettes/example_report.Rmd so that it just renders the markdown landing page for EpiArchives.

Bug fixes

• README.Rmd:
  • Fix broken link to example report.
• test-EpiCompare.R:
  • Fix issue with PNG save path.
  • Make separate subfolders for each set of tests.
• test-output_files.R
  • Make separate subfolders for each set of tests.
• plot_enrichment
  • Conditionally generate plots only when enrichment results aren't NULL.
  • Return KEGG/GO enrichment results as well as the plots.
• Add workers <- check_workers(workers = workers) to all functions that take workers to handle workers=NULL properly.

EpiCompare 1.3.3

New features

• download_button:
  • Saves and downloads files.
• prepare_blacklist:
  • Auto-selects appropriate blacklist, or returns user-specified option.
  • EpiCompare(blacklist=NULL) is now the default.
• prepare_genome_builds:
  • Update to handle supplying builds for "peakfiles" and "reference" but not "blacklist" (so long as the blacklist arg is not a user-supplied GRanges object)
• Added mm9_blacklist
• Made more plots interactive:
  • width_boxplot
  • plot_enrichment
  • plot_ChIPseeker_annotation
• overlap_stat_plot
  • Name elements in output list.
• Change annotation arg to more informative txdb arg, and set default to NULL, which ChIPseeker functions will automatically handle.
• New function as_interactive:
  • Help standardise this.
• New EpiCompare::EpiCompare arguments:
  • error: keep knitting even on errors.
  • tss_distance: upstream/downstream of TSS.
  • quiet: knit quietly
• Rename 'test-EpiCompare_combinations.R' --> 'test-EpiCompare.R'
• Separate test-generalMetrics_functions.R into function-specific test files.
• Separate test-peakOverlap_functions.R into function-specific test files.
• Make fancy header with new func:
  • report_header()
• Create EpiCompare command code as text:
  • report_command()
• width_boxplot:
  • Make more efficient with data.table and lapply
• Update hex sticker to match custom.css palette.
• README.Rmd
  • Collapse more detailed sections.

Bug fixes

• tss_plot:
  • Fix examples/tests after Sera updated the arguments.
  • Pass upstream/downstream to ChIPseeker::getTagMatrix
  • Make interactive
  • Name plots in list
  • Remove unnecessary extra level of list nesting.
• Make documentation width <80 lines where possible.
• EpiCompare.Rmd
  • Remove methods::show from all parts
  • Name all chunks
  • Make explanations more clear
  • Add table of contents for main 3 sections.
  • Fix header levels
  • Set results='asis' globally instead of in each chunk header.
  • Automatically number sections with yaml arg: number_sections: true
  • Omit specific headers from numbering system with {-} tags.
  • Add custom.css
• plot_chromHMM:
  • Error in (function (classes, fdef, mtable) unable to find an inherited method for function ‘annotateWithFeatures’ for signature ‘"SimpleGRangesList", "list"’
  • Misleading error message; was actually due to chromHMM_annotation not being converted from a list to a GRangesList.
  • Change yaml arg peakfile --> peakfiles to be consistent with other variables.

EpiCompare 1.3.1

New features

• Replace badger with rworkfows:
  • Use rworkflows::use_badges
• New helper functions:
  • precision_recall_matrix
  • report_time
• overlap_upset_plot:
  • Switched out UpSetR for ComplexUpsetto show percentages.
  • Moved up dep checks to beginning of function.
• Handle bug with heatmaply by checking args where it might be used:
  • check_heatmap_args
• tss_plot:
  • Add unit tests
  • Drastically reduce example/test runtime by setting upstream=50
• compute_corr:
  • Reduce example runtime by setting bin_size = 200000 (takes <2s).

Bug fixes

• Fix typo in EpiCompare docs: "hg38 blacklist dataset"
• Avoid explicitly specifying "/" in paths to help cross-platform testing.
• tss_plot:
  • Use parallel::detectCores-1 by default to set workers, but set to 1 in examples/tests to meet CRAN/Bioc standards.

EpiCompare 1.1.4

New features

• Add back example report html:
  • Put it in the main dir
  • Add it to the .Rbuildignore: report/EpiCompare_example.html
  • Add a new vignette that renders the HTML from the pre-saved file.
• Remove Dockerfile, as it's no longer necessary with the updated version of rworkflows

Bug fixes

• Add @returns to group_files function.
• Add all authors to vignettes.

EpiCompare 1.1.3

New features

• New function: predict_precision_recall
  • Added unit tests.
• compute_corr and precision_recall now save outputs, including when run via EpiCompare Rmarkdown script.
• Make subfunctions for plot_precision_recall:
  • plot_precision_recall_prcurve
  • plot_precision_recall_f1
• rebin_peaks:
  • Allow users to specify sep between genomic coordinates in rownames.

Bug fixes

• Update gather_files to match new Picard file scheme in nf-core/cutandrun 3.0.

EpiCompare 1.1.2

New features

• rebin_peaks:
  • Added arg drop_empty_chr to automatically drop chroms that aren't in any of the peakfiles.
  • Added "score" as one of the default intensity_cols in all relevant functions.
  • Make examples use 5000bp bins to speed up.
• translate_genome:
  • Add default_genome arg to handle genome=NULL.
• bpplapply:
  • New exported function to automate handling of known issues with BiocParallel across OS platforms.
  • Enable users to specify their own apply function.
• get_bpparam: Add args to allow users to choose which BiocParallel func to use.
• checkCache: Make default arg cache=BiocFileCache::BiocFileCache(ask = FALSE) to skip user input during runtime.
• precision_recall:
  • Change increment_threshold arg to n_threshold arg, using the seq(length.out=) feature to avoid accidentally choosing an inappropriately large increment_threshold.
• gather_files:
  • Replace iterator with bpplapply.
  • Pass up args from bpplapply.
  • Provide warning message, not error, when 0 files found. Returns NULL.
  • Add "multiqc" as a search option.
  • Add dedicated subfunctions for reading in a variety of nf-core/cutandrun outputs files: read_picard,read_multiqc,read_bowtie, read_trimgalore,read_bam,read_peaks
  • Add file paths to each object.
  • Add new arg rbind_list.
• rebin_peaks/compute_corr: -Change defaultbin_size from 100 --> 5kb to improve efficiency and align with other defaults of other packages (e.g Signac).
• tss_plot:
  • Pass up more arg for specifying upstream/downstream.
• EpiCompare: Pass up new args:
  • bin_size
  • n_threshold
  • workers

Bug fixes

• Fix rebin_peaks unit tests.
• Fix pkg size issue by adding inst/report to .Rbuildignore.
• EpiCompare wasn't being run when reference was a single unlisted GRanges object because it was indeed length>1, but the names were all NULL. Now fixed.
• plot_precision_recall: Set default initial_threshold= to 0.
• Switch from BiocParallel to parallel, as the former is extremely buggy and inconsistent.

EpiCompare 1.1.1

New features

• check_genome_build: Add translate_genome as prestep.
• rebin_peaks:
  1. Move all steps that could be done just once (e.g. creating the genome-wide tiles object) outside of the BiocParallel::bpmapply iterator.
  2. Ensure all outputs of BiocParallel::bpmapply are of the same length, within the exact same bins, so that we can return just the bare minimum data needed to create the matrix (1 numeric vector/sample).
  3. Instead of rbinding the results and then casting them back into a matrix (which is safer bc it can handle vectors of different lengths), simply cbind all vectors into one matrix directly and name the rows using the predefined genome-wide tiles.
  4. Because we are no longer rbinding a series of very long tables, this avoids the issue encountered here #103. This means this function is now much more scalable to many hundreds/thousands of samples (cells) even at very small bin sizes (e.g. 100bp).
  5. A new argument keep_chr allows users to specify whether they want to restrict which chromosomes are used during binning. By default, all chromosomes in the reference genome are used (keep_chr=NULL), but specifying a subset of chromosomes (e.g. paste0("chr",seq_len(12))) can drastically speed up compute time and reduce memory usage. It can also be useful for removing non-standard chromosomes (e.g. "chr21_gl383579_alt", "chrUns...", "chrRand...").
  6. As a bonus, rebin_peaks now reports the final binned matrix dimensions and a sparsity metric.

• compute_corr:
  • Added unit tests at different bin sizes.
  • Allow reference to be NULL.
• Updated README to reflect latest vesion of EpiCompare with gather_files.

Bug fixes

• Bumped version to align with Bioc devel (currently 1.1.0).
• compute_percentiles:
  • Making default initial_threshold=0, so as not to assume any particular threshold.
• rebin_peaks:
  • Addressed error that occurs when there's many samples/cells with small bins.
• plot_precision_recall: Don't plot the reference as part of the PR curve.

EpiCompare 0.99.21

Bug fixes

• Changed terminology from "epigenetic" to "epigenomic"
• Updated README to include precision_recall_plot and corr_plot
• Removed bugs in html report
• Added example EpiCompare report in inst/report/EpiCompare_example.html

EpiCompare 0.99.20

New features

• Upgraded liftover_grl and added genome standardization.
  • Enable cross-species liftover from/to mm10 and mm9 --> hg19 and hg38.
  • Subfunctionalize get_chain_file.
  • Add merge_all option.
• Support mm10/mm9 as output_build options.
• Removed dplyr.
• Moved plyranges to Suggests.
• plot_precision_recall:
  • New exported function to create precision-recall plots from MACS2, MACS3, HOMER, or SEACR peak files.
  • Added unit tests.
  • Added to EpiCompare html report.
  • Added EpiCompare(precision_recall_plot=) param and documented.
• Add ISSUE templates.
• Include code in html report (collapsed by default).
• Add correlation matrix/plot functionality.
• Add compute_consensus_peaks() as function for preprocessing peak files.
  • Add group_files() function to help assign each peakfile to a group based on substring searches.
• EpiCompare:
  • Return paths to HTML reports.
  • Automatically open report in browser or rstudio.
• Add Docker vignette and advertise in README.

Bug fixes

• Made BiocParallel functions compatible with Windows.
• Organize author fields in DESCRIPTION.
• Fix typos in README.
• Remove threshold=1 from list of thresholds to test in precision-recall curves.
• Set first chunk in EpiCompare.Rmd as echo=FALSE instead of include=FALSE so the output messages will still be printed (without showing the code).
• Remove here from Suggests.
• Fix directory creation in EpiCompare::EpiCompare.

EpiCompare 0.99.19

Bug fixes

• Simplified loops with mapply/lapply.

New features

• EpiCompare: accepts multiple reference files - creates individual reports for each reference. Added timing feature.
• save_output(): this function saves all plots and tables generated by EpiCompare. Also saves interactive heatmaps. Used in EpiCompare.Rmd.
• fig_length(): This function outputs dynamic figure height/width depending on the number of items. Used in EpiCompare.Rmd.

EpiCompare 0.99.18

Bug fixes

• prepare_reference: Validate reference input before passing to next step.
• Pass named list to genome_build to allow for different builds between reference and peaklist.
• Liftover blacklist to match GRanges list it's being used to filter in tidy_peakfile.
• Ensure all names are unique in peaklist and reference.
• gather_files:
  • Avoid gathering duplicates peak files from nf-core/cutandrun.
  • Add progress bar.
  • Add report at the end.
  • Add extra arg return_paths to return only the paths without actually reading in the files.

New features

• Overhaul how EpiCompare handles genome builds:
  • New argument genome_build_output allows users to specify which genome build to standardise all inputs to.
  • genome_build can now take a named list to specify different genome builds for peakfiles, reference, and blacklist.
  • Added functions to parse and validate all genome build-related arguments.
• Remove unnecessary deps.
• Use data.table to read/write tables.
• prepare_peaklist:
  • Simplified code.
  • Added arg remove_empty to automatically drop any empty elements.
  • Embed check_list_names within.
• plot_chromHMM:
  • Can return data as well with return_data.
  • Performs liftover on chromHMM data instead of the peaklist.

EpiCompare 0.99.17

Bug fixes

• Make output_dir creation recursive and without warnings.
• Add new params to Code section of rmarkdown output.

New features

• Add new peaklist length check to prepare_peaklist.
• New check functions:
  • check_genomebuild: ensure necessary packages installed and that "genomebuild" is valid.
  • check_cell_lines
• liftover_grlist: Dedicated liftover function, exported.
• Document checkCache.
• get_chromHMM_annotation can now take a list of cell lines as an argument.

EpiCompare 0.99.16

Bug fixes

• Fix GHA pkgdown building:
  • The newest version of git introduced bugs when building pkgdown sites from within Docker containers (e.g. via my Linux GHA workflow). Adjusting GHA to fix this.

EpiCompare 0.99.3

New Features

• New functions with examples/unit tests:
  • import_narrowPeak: Import narrowPeak files, with automated header annotation using metadata from ENCODE.\
  • gather_files: Automatically peak/picard/bed files and read them in as a list of GRanges objects.\
  • write_example_peaks: Write example peak data to disk.
• Update .gitignore
• Update .Rbuildignore

EpiCompare 0.99.1

New features

• New parameter in EpiCompare:
  • genome_build: Specify the genome build, either "hg19" or "hg38". This parameter is also included in plot_chromHMM, plot_ChIPseeker_annotation, tss_plot and plot_enrichment.

EpiCompare 0.99.0

New Features

• EpiCompare submitted to Bioconductor.