Changelog

Source: NEWS.md

echodata 0.99.17

New features

  • melt_finemapping_results:
    • Check to see if already melted.
  • Update rworkflows.yml

Bug fixes

  • portal_query:
    • Ensure files_filt is in data.table format.
  • reassign_lead_snps
    • Ensure merged_dat is in data.table format.
  • parquet functions:
    • Remove unit tests for now, as they cause segfault errors during checks (but not when run manually).

echodata 0.99.16

New features

  • Use rworkflows GHA.
  • Moved all GitHub-related functions to new package: echogithub
    • Kept portal-related function in echodata: e.g. portal_query

Bug fixes

  • use remote MungeSumstats until it passes bioc devel again

echodata 0.99.15

New features

  • import_topSNPs:
    • Automatically downloads data is topSS is a remote file.
    • New arg startRow for skipping rows.
  • check_if_empty –> is_empty (more concise)
  • get_data:
    • Allow users to specify tag and … args.
  • get_header can read parquet now.

Bug fixes

  • standardize_maf:
    • Fix flaw in logic preventing MAF being imputed from Freq.
  • standardize_proportion_cases:
    • When colmap$proportion_cases is NULL, just return query.
  • Fix GHA: @master –> @v2
  • Fix reassign_lead_snps warnings.
  • Fix biomart_geneInfo warnings.
  • Fix is_url example.
  • gene_locus_list:
    • Drop loci missing from topSNPs.
  • Fix melt_finemapping_results:
    • Alphanumerically sort Methods col consistently via new internal function: order_methods

echodata 0.99.14

New features

  • get_sample_size:
    • Add more complete documentation on what happens when “N” column is present.
    • Add extra check to make sure MungeSumstats >=1.3.9 is installed.
    • compute_n can now be a numeric vector of length equal to nrow(dat).
  • is_url:
    • New export function.
    • User-specified URL protocols to search for.

Bug fixes

  • Make R.utils an Import to avoid any issues with reading gz files.
  • Make sure standardize uses construct_colmap to rename “N” column.

echodata 0.99.13

New features

  • New function: get_Kunkle2019_coloc.
  • Remove zscore* functions (not used anymore).
  • standardize_gene_locus_cols: Will replaced Locus names with new Locus_Gene naming scheme when grouping_vars contain both Locus and Gene.
  • Move over functions from echoannot:
    • get_SNPgroup_counts
    • results_report
    • merge_finemapping_results
  • portal_query: add arg to return results in table format.
  • Export get_data
  • get_Nalls2019_loci:
    • Add limit_snps arg = Save tempdir() instead of cache by default, to allow subsetting different numbers of SNPs more easily.
    • Add force_new arg.

Bug fixes

  • portal_query: Forgot to add sep= name in URL construction.
  • get_sample_size: Fix unit tests.
  • get_header: Fix misnamed variable.

echodata 0.99.11

New features

  • Pass up compute_n as arg in standardize.
  • Add get_Nalls2019_coloc function.

Bug fixes

  • get_sample_size: Return NULL when “N” col not present at end of func. Otherwise, max(NULL) can give you -Inf.

echodata 0.99.10

New features

  • Remove MungeSumstats from Remotes.
  • Passing all CRAN checks.
  • Cache datasets.
  • New get_Nalls2019_loci function, to easily write example loci to disk and return paths.

Bug fixes

  • Use paste instead of file.path to construct portal query URLs.

echodata 0.99.9

New features

  • get_header: Can now handle VCFs (assuming #CHROM is the comment char).
  • Moved get_CS_bins and get_CS_counts from echoannot –> echodata.
  • Passing all CRAN checks!

Bug fixes

echodata 0.99.8

New features

  • construct_colmap: Collapses many column mapping args into one function.
  • standardize_subset –> standardize:
    • Simplified workflow.
    • Operates on only query instead of both query and query_mode.
    • Created subfunctions for each step.
    • Removed liftover step.

echodata 0.99.7

New features

  • New functions:
    • preview
    • is_local
    • is_url
  • Increased test coverage to >88%.
  • Removed standardise_sumstats_column_headers_crossplatform to use directly from MungeSumstats.

Bug fixes

  • import_topSNPs:
    • Now uses standardise_sumstats_column_headers_crossplatform exported function when munge=TRUE.
    • Both standardisation strategies no longer interfere with one another when used at the same time.

echodata 0.99.6

New features

  • Added .zzz file with .datatable.aware <- TRUE
  • Added new function merge_robust to address issues with data.table.
  • import_topSNPs: Added example and documented all params.
  • Rename MUNGESUMSTATS.* functions to mungesumstats_.
  • get_sample_size: Add unit tests and new return_only function for min/max.

echodata 0.99.5

New features

  • Added new functions (with unit tests):
    • snp_group_colorDict
    • read_parquet
    • write_parquet

Bug fixes

  • reassign_lead_snps: Handle situations where none of the grouping_vars are available.
  • Fix error in reporting number of Consensus_SNPs in find_consensus_snps (only affected console message, not the actual data).

echodata 0.99.4

New features

  • Added new functions (with unit tests):
    • snp_group_filters
    • find_consensus_SNPs
    • find_consensus_SNPs_no_PolyFun
    • filter_snps
    • limit_SNPs
    • gene_trimmer
    • fillNA_CS_PP
    • determine_chrom_type
    • is_empty
    • column_dictionary
    • get_header
    • melt_finemapping_results
    • update_cols
    • biomart_geneInfo
    • find_top_consensus
    • dt_to_granges
    • is_granges
    • is_ggplot
    • is_ggbio
    • granges_to_bed
    • reassign_lead_snps

echodata 0.99.3

New features

  • Added new function coords_to_rsids, copied over from catalogueR.

echodata 0.99.2

New features

  • Added a NEWS.md file to track changes to the package.
  • Added new function assign_lead_SNP with unit tests.
  • Added unit tests for createDT and MUNGESUMSTATS.* functions.
  • Removed unused functions.
  • Added dynamic badges to README.

Bug fixes

  • Updated GHA workflow.
  • Added GH token to Secrets.

echodata 0.99.0

New features

  • Large datasets uploaded/downloaded via piggyback.

echodata 0.99.0

New features

  • Functions extracted from echolocatoR to create echodata.