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echolocatoR 3.0.0

New features

  • Remove deprecated finemap_pipeline() wrapper.

Bug fixes

  • Fix Rd formatting and \dontrun{} example guards.
  • Add Rplots.pdf and *.tbi to .gitignore.
  • Remove tracked .DS_Store files.

echolocatoR 2.0.5

Bug fixes

  • Local R CMD check fixes and compatibility updates.

echolocatoR 2.0.4

New features

  • Standardize rworkflows.yml with canonical template: enable Docker on ghcr.io, set write-all permissions, use GITHUB_TOKEN, remove docker_user/docker_org/DOCKER_TOKEN, add devel branch trigger.
  • Remove tracked .DS_Store files.

echolocatoR 2.0.3

New features

  • Implement new rworkflows version of GHA.
  • Remove Dockerfile.
  • Move "plot_locus.Rmd" vignette to echoplot.
  • Add notes on susieR installation issues to README.

echolocatoR 2.0.2

New features

  • Add new internal function: check_topSNPs
  • Impute MAF when.
  • Fully documented all functions.
  • Updated manual.
  • finemap_loci:
    • Throw an error when no loci are available to fine-map after locus filtering.
  • Passing all CRAN checks for the first time!!
  • Allow more args to have >1 input (and make these vars more consistently named):
    • n_causal_i
    • bp_distance_i
    • LD_genome_build_i
  • Create dedicated echolocatoR docker/singualarit container:
    • Add docker vignette
    • Update README

Bug fixes

  • Improve handling of conditioned_snps in various scenarios.
  • Fix GHA: @master --> @v2
  • Fix vignettes:
    • plot_locus
  • Fix Error in .new_IRanges_from_start_end(start, end): 'start' or 'end' cannot contain NAs
    • Was due to loci not present in topSNPs being included. Now handled by echodata::gene_locus_list.
  • Add Suggests used in vignettes: ggplot2,patchwork
  • check_genome:
    • Omit tests that require large optional databases to be installed.
    • Update dbSNP default to 155.
  • README
    • Set echofinemap::required_cols(add_versions = FALSE,...) to avoid issues with not being able to find PolyFun/PAINTOR installations during rendering.

echolocatoR 2.0.1

New features

  • New args in finemap_loci:
    • seed
    • priors_col
  • Pass compute_n to echofinemap::multifinemap.
  • echoplot updates:
    • Passed up new arg from echoplot::plot_locus(tx_biotypes=).
    • Changed arg qtl_prefixes --> qtl_suffixes.
    • Passed up show_plot to finemap_loci.
    • Fixed 0 transcripts bug.
  • Can now supply LD_reference with a list of vcf/csv/tsv/txt files (and their compressed versions), or rda/rds files.

Bug fixes

  • Fix typo in tryCatch in finemap_loci.
  • Deprecate PAINTOR_QTL_datasets arg.
  • finemap_locus: Recording args causing an error every time (object 'locus' not found) even when wrapped in tryCatch. Setting arguments <- NULL for now.
  • Fix old arg in: plot.types --> plot_types

echolocatoR 2.0.0

New features

  • Split echolocatoR into task-specific sub-packages ("modules"). See details here.
  • Collapse column-name mapping args into one argument: construct_colmap
  • Added a NEWS.md file to track changes to the package.
  • QTL studies now supported by finemap_loci.
  • Remove inst/tools and moved to echofinemap as git submodules.
  • Add startup message.
  • Add messages with icons for each step.
  • Record arguments as a named list and include it in the results list.
  • Add (interim) Docker/Singularity instructions to README.

Bug fixes

  • FINEMAP:
    • File parsing issues, esp across FINEMAP versions.
    • dylib errors
    • Multiple CS per SNP