NEWS.md

In RajLabMSSM/echolocatoR: Automated genomic fine-mapping

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

RajLabMSSM/echolocatoR documentation built on Jan. 29, 2023, 6:04 a.m.