NEWS.md

In RajLabMSSM/echoannot: echoverse module: Annotate fine-mapping results

echoannot 0.99.11

New features

• Implement rworkflows

echoannot 0.99.10

New features

• annotation_file_name:
  • New export function.
• ROADMAP_merge_and_process_grl --> ROADMAP_merge_and_process
• ROADMAP_query:
  • Embed ROADMAP_merge_and_process as an option.
  • Make save_path more unique by adding params to name.
• ROADMAP_tabix:
  • Can now find a read in existing files of the same.
• XGR_query --> XGR_query:
  • Embed n_top as an option, passed to XGR_filter_assays and XGR_filter_sources.
• xgr_query --> xgr_example (to avoid conflict with func name)
• Move functions to echoplot:
  • ROADMAP_plot and plotting subfunctions.
  • XGR_plot and plotting subfunctions.
• Move functions to downloadR:
  • zenodo_upload
  • zenodo_list
• Remove Imports:
  • scales
  • piggyback
  • RColorBrewer
  • zen4R
• test_enrichment:
  • Can convert data.tables to GRL too.
  • Pass up args from PermTest: min.parallel,force.parallel
  • Allow users to set seed.
• Move zenodo_list to downloadR

Bug fixes

• ROADMAP_query: rtracklayer::import has some bugs that prevent it from importing certain bed.gz files. So implemented a workaround using custom functions instead.
• Reduce vignette sizes to <5Mb.
• Fix super_summary_plot unit tests.
• Switch website to gh-pages branch.
• Fix GHA: @master --> @v2
• NOTT2019_plac_seq_plot:
  • Get rid of hjust warning.

echoannot 0.99.9

New features

• Added MOTIFBREAKR suite of functions.
  • MOTIFBREAKR,MOTIFBREAKR_calc_pvals,MOTIFBREAKR_filter, MOTIFBREAKR_plot,MOTIFBREAKR_summarize
  • Fully documented.
  • First attempts to get parallelization working.
  • Passes up other args from motifbreakR core functions.
  • Saves motif plots as PDFs.
• Added get_bpparam function.
• Added filter_chromatin_states function (internal).
• Move to echodata package:
  • get_SNPgroup_counts
  • results_report
  • merge_finemapping_results: and split annotation portions into new annotate_snps.

Bug fixes

• get_SNPgroup_counts:
  • Get rid of .dots and .groups warnings.
• Update main vignette to reflect all changes.
• annotate_snps: Fix subfunctions (there's been some updates to tool outputs).
• Fix ROADMAP_query.

echoannot 0.99.8

New features

• Split peakyfinders from echoannot.
• cell_type_specifity: Derive a EWCE-inspired specificity score for each cell-type and show in plot.

Bug fixes

• merged_finemap_results: Fix overwriting multifinemap_pattern.

echoannot 0.99.7

New features

• import_peaks_geo:
  • Can now import/call peaks in parallel, by splitting queries across chromosomes.
  • Can now import >1 peak type at a time, and documents it in "peaktype" col.
• import_peaks:
  • Pass up args: regex_queries, split_chromosomes
• New function: process_ids:
  • Able to get GSM sample names from GSE project ID.
• Split import_peaks_geo into separateimport_peaks_* functions for each file type.

Bug fixes

• When only one peak type is returned from GEO search, prevent mapply from turning the results into a matrix with SIMPLIFY=FALSE.
• Return empty GenomicRanges::GRanges() instead of error/NA/NULL during errors, so you can still merge at the end.

echoannot 0.99.6

New features

• XGR_query: Set dat=NULL to return genome-wide data.
• New vignette: cell_type_specific_epigenomics, with Nott2019 and Corces2020 data.

Bug fixes

• prepare_highlight_plac_data: Allow to plot overlap with any SNP group (not just consensus SNPs).

echoannot 0.99.5

New features

• Moved get_CS_counts/get_CS_bins to echodata.
• Cache remote data resources in echoannot-specific folder.
• Add XGR GitHub installation again (CRAN installation not working again?).
• Shorten Nott2019 ref links.
• Pass all CRAN checks.

Bug fixes

• Added R.utils/tools to Imports.
• Added GEOquery/regioneR/ BSgenome.Hsapiens.UCSC.hg38/BSgenome.Hsapiens.UCSC.hg19 to Suggests.
• Updated GHA workflow to account for git security changes.
• Fixed convert_plots when converting Tracks to list of ggplots.
• Fixed merge_celltype_specific_epigenomics
  • Added caching mechanism.
• Use echodata::<locus> data instead of portal data for Getting started vignette.
• Replace file.path with paste.
• Replace "echoR" with "echoR_mini".
• Set timeout with multiple approaches: options,httr::timeout, httr::config.

echoannot 0.99.4

New features

• New functions
  • import_peaks: Search for peak files in GEO/ENCODE, or compute them from bedGraph files.
  • call_peaks: Call peaks from bedGraph files using MACSr.
  • test_enrichment: Run permutation enrichment tests.

echoannot 0.99.3

Bug fixes

• Update to match latest echotabix changes.
• Update GHA workflow.

echoannot 0.99.3

New features

• Added function convert_plots.

Bug fixes

• Move as many Imports to Suggests as possible.
• GHA servers can't install XGR from CRAN. Switching to GitHub remote installation until they fix this.
• Removed docs/ folder.
• Reduced vignette size.
• Transition all usage of ggplot2 to requireNamespace method to reduce NAMESPACE.
• Make all new col assignments in GRanges objects use the proper mcols syntax.
• Make sure all GRanges in UCSC format in NOTT2019_plac_seq_plot.
• Subdivide NOTT2019_plac_seq_plot into subfunctions.
• New exports:
  • NOTT2019_get_epigenomic_peaks

echoannot 0.99.2

New features

• Added a NEWS.md file to track changes to the package.
• Replace the following with echoverseTemplate versions:
  • New hex logo.
  • GHA
  • README
  • Vignette header
• Offload functions to echodata:
  • assign_lead_snp
  • find_consensus_snps
  • update_cols
  • biomart_geneInfo
  • find_top_consensus
  • dt_to_granges
  • is_granges
  • granges_to_bed
  • reassign_lead_snps
• Renamed all functions to exclude ".":
  • "ROADMAP." --> "ROADMAP_"
  • "NOTT_2019." --> "NOTT2019_"
  • etc.
• Added xgr_example example data.
• Added unit tests for super_summary_plot and its subfunctions.
• Offloaded all liftover functions to echotabix
• Made new wrapper functions to simplify importing/plotting pipelines:
  • XGR_plot
  • ROADMAP_plot

RajLabMSSM/echoannot documentation built on Oct. 26, 2023, 2:41 p.m.