NEWS.md

In RajLabMSSM/echodata: echoverse module: Fine-mapping data access and formatting

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

• 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.

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.
  • See here for Issues: https://github.com/RajLabMSSM/echolocatoR/issues/72#issuecomment-1059423642
• 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.

RajLabMSSM/echodata documentation built on Nov. 21, 2023, 8 a.m.