pQTLtools v0.3
- 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().