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Changelog

Source: NEWS.md

pQTLtools 0.5

(2025/3/25)

  • Add single quotes to package/software name.
  • Add inst/scripts for docs.sh and cran.sh.
  • Drop link to GitHub repository in _pkgdown.yml and a lot of options().
  • Merge Bioconductor-related and LocusZoom.js/SCALLOP-Caprion articles.
  • Revise README.Rmd/bioconductor.Rmd/pQTLtools.Rmd to suppress Fedora 41 check.
  • Set fig.height/fig.width for articles and suggest Cairo for CairoPNG.
  • Suggests CAMERA, MSnbase, MSstats, mzR, protViz, rawrr, Spectra

pQTLtools 0.4

(2025/3/7)

  • Another pass through R CMD check –as-cran
  • Revise articles esp. pQTLtools, esse, LocusZoom.js (including lz.html and stack.html).
  • Unify DESCRIPTION/README.md (finally).
  • Add support for MathJax and mermaid.
  • Add Caprion coloc scripts.
  • Add SummarizedExperiment section to es.Rmd –> esse.Rmd.
  • Add csq(), protein_altering_variants (so data/), histo.fyi, aria-label.
  • Adopt new hg38 LD blocks for turboman().
  • Add spectrum.Rmd.
  • Renew call to ldops in novelty_check() in accordance with ieugwasr.
  • Replace tests/ with most recent PROC results.

pQTLtools 0.3

(2024/05/26)

  • Activate package logo for the GitHub repository.
  • Dedicated .R files for (blocks of) functions.
  • Use of scope operator for clarification, e.g., ensembldb::genes().
  • Use of OPENGWAS_JWT (.Renviron) from https://api.opengwas.io/profile/.
  • Suggest IlluminaHumanMethylation450kmanifest, OUTRIDER.
  • Fix URL in DESCRIPTION/snakemake.Rmd.

pQTLtools 0.2

(2024/04/24)

Milestones

  • 2023.12. Add LocusZoom.js article.
  • 2023.05. Test data are fully available with medRxiv post of the SCALLOP paper.
  • 2022.12. A new package pQTLdata is created to hold panel and meta data.
  • 2022.06. It passes CRAN checks with no warning.
  • 2021.02. A web-driven documentation is now available, https://jinghuazhao.github.io/pQTLtools/.

Package

The information here mirrors the package DESCRIPTION,

  • Depends R (>=3.5.0), pQTLdata.
  • Import dplyr, gap, ggplot2, Rdpack.
  • importFrom utils read.table tail.
  • Import from lmm as template, use save(compress=‘xz’).
  • Replace ChangeLog with NEWS.md.
  • LICENSE.md and README.md.
  • Reduce size by sed -i '/ISSN/d' REFERENCES.bib.
  • Suggest Biobase, BioStrings, GenomeInfoDb, GenomicRanges, IRanges, VariantAnnotation.
  • Suggest Roxygen2.
  • Suggest biomaRt, bookdown, circlize, cowplot.
  • Suggest gap.datasets, gwasvcf, htmlwidgets, httr, ieugwasr.
  • Suggest knitr, mclust, meta.
  • Suggest openxlsx, plotly, plyr.
  • Suggest regione, rgl, rmarkdown, rtracklayer.
  • Suggest scatterplot3d, seqminer, stringr.
  • GitHub action
  • inst/Bioconductor/.
  • inst/STRING/change_STRING_colors.py.
  • inst/UniProt|PPI/README.md.
  • inst/snakemake
  • pQTLtools.Rmd, bioconductor.Rmd, es.Rmd, LocusZoom.js.Rmd, snakemake.Rmd and SCALLOP-INF.Rmd articles.
  • List publications on pQTLs by Sun et al. (2018) and Suhre et al. (2020).

Functions

The list is in no particular order,

  • peptideMapping(), peptideAssociationPlot().
  • make_ExpressionSet(), novelty_check(), qtl_lookup(), turboman(), turboqq().
  • Reflow turboman.r/[partial]turboqq.r by formatR::tidy_source().
  • pqtlMR(), run_TwoSampleMR().
  • run_coloc().
  • import_OpenGWAS()
  • import_eQTLCatalogue().
  • genequries(), regionqueries(), snpqueries().
  • uniprot2ids().

pQTLtools 0.1

  • First release