NEWS.md

In jinghuazhao/pQTLtools: A Protein Quantitative Trait Locus Toolkit

pQTLtools 0.3

• Use scope operator for clarification, e.g., ensembldb::genes()
• Mask TwoSampleMR example due to problem with OPENGWAS_JWT from https://api.opengwas.io/profile/
• Suggest IlluminaHumanMethylation450kmanifest, OUTRIDER
• Fix URL in DESCRIPTION/snakemake.Rmd

pQTLtools 0.2

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

jinghuazhao/pQTLtools documentation built on May 18, 2024, 12:14 p.m.