NEWS.md

In RajLabMSSM/catalogueR: QTL data extraction and colocalization

catalogueR 1.0.1

New features

• Implement rworkflows.

catalogueR 1.0.0

New features

• Offload functions to echoverse deps:
• get_data() --> echodata
• get_os() --> echodata
• load_rdata() --> downloadR
• example_sumstats_paths() --> echpdata::get_Nalls2019_loci()
• find_consensus_SNPs --> echodata::find_consensus_snps()
• locus_plot --> echoplot
• Rename functions to fit echoverse conventions:
• Remove "." from any function names.
• All eQTL Catalogue functions start with eQTLcatalogue_.
• All COLOC functions start with COLOC_.
• Deprecated all functions properly to let users know.
• Change arg in all functions:
• gwas_data --> query_granges
• genome_build --> query_genome
• Condensed multiple arguments into echotabix::construct_query()
• gwas.data, chrom, bp_min, bp_max
• New exported functions:
• COLOC_heatmap
• COLOC_corplot

Bug fixes

• Updated function/arg names from echoverse deps.
• Updated meta data to include latest paths and datasets.
• fix_ftp: Replacing "ftp:" prefix with "http:" seems to drastically improve the ability of functions to query the files.

catalogueR 0.1.1

New features

• Added a NEWS.md file to track changes to the package.
• Split functions into separate files.
• Made README into .Rmd file.
• Changed license to GPL-3 and removed LICENSE file.
• Removed old data.table version requirement (issues with compressed files have since been resolved).
• Updated .Rbuildignore and .gitignore
• Added GitHub Actions via biocthis::use_bioc_github_action(pkgdown_covr_branch = c("main","master")).
• Replaced T/F with TRUE/FALSE in accordance with best coding practices.
• Replaced NAMESPACE file with Roxygen-generated version.
• Replaced internal functions with echoverse packages:
• echotabix
• echoconda
• Replaced built-in datasets with echodata datasets:
• BST1
• LRRK2
• MEX3C
• Styled code with: styler::style_pkg(transformers = styler::tidyverse_style(indent_by = 4))
• Replace printer with messager.
• Created dev branch.
• Add GTEX_v8 metadata to eQTL_Catalogue.list_datasets.
• Example coloc results now accessed via get_coloc_QTLs:
• Moved coloc_QTLs_full to Releases as it was >12Mb.
• Moved coloc_QTLs to Releases as it was >1.5Mb.
• Moved eQTL Catalogue query results to Release via example_eQTL_Catalogue_query_paths.
• Replace liftover functions with echotabix::liftover (removed unused deps).
• Replaced rsids_from_coords with echodata::coords_to_rsids (removed unused deps).
• Made "REST" default method for all relevant functions.
• Deprecated:
• gather_files in favor of more descriptive merge_files
• gather_colocalized_data in favor of more descriptive merge_colocalized_data

Bug fixes

• Reduced NAMESPACE by properly exporting functions.
• Removed library calls within functions.
• Added requireNamespace where suggests are used.
• Changed eQTL_Catalogue.query so that the default is use_tabix=FALSE due to instability of using tabix with the EBI server. See here for details.
• run_coloc automatically infers (effective) sample size and checks that MAF is present for all SNPs (after removing MAF>=1 or <=0 or ==NA).
• Removed example query results (e.g. MEX3C__Alasoo_2018.macrophage_IFNg) from built-in data as these were already included in exdata.

catalogueR 0.1.0

First version of catalogueR created as a sister package of echolocatoR.

RajLabMSSM/catalogueR documentation built on Jan. 1, 2023, 10:45 a.m.