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Package: mrpipeline 0.1.0

Jamie Robinson

mrpipeline: Implements a Ready-for-Use Mendelian Randomisation Pipeline

This package implements a pipeline which in turns allows for simple and generally "hands-free" Mendelian randomisation analyses to be run. Data may be used from the OpenGWAS DB or locally, using .vcf files. Analyses include MR, colocalisation and standard MR sensitivity analyses. Please see the documentation for more details.

Authors:Jamie Robinson

mrpipeline_0.1.0.tar.gz
mrpipeline_0.1.0.zip(r-4.7)mrpipeline_0.1.0.zip(r-4.6)mrpipeline_0.1.0.zip(r-4.5)
mrpipeline_0.1.0.tgz(r-4.6-any)mrpipeline_0.1.0.tgz(r-4.5-any)
mrpipeline_0.1.0.tar.gz(r-4.7-any)mrpipeline_0.1.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
card.svg |card.png
mrpipeline/json (API)

# Install 'mrpipeline' in R:

install.packages('mrpipeline', repos = c('https://mrcieu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jwr-git/mrpipeline/issues

On CRAN:

3.07 score 6 stars 39 scripts 23 exports 148 dependencies

Last updated from:2c84a8deaa. Checks:8 ERROR, 1 FAIL. Indexed: no.

Target	Result	Time
linux-devel-x86_64	ERROR	189
source / vignettes	ERROR	316
linux-release-x86_64	ERROR	202
macos-release-arm64	ERROR	162
macos-oldrel-arm64	ERROR	156
windows-devel	ERROR	126
windows-release	ERROR	144
windows-oldrel	ERROR	114
wasm-release	FAIL	140

Exports:%>%annotate_efo annotate_ensg calc_f_stat check_snps cis_trans combine_results dat_to_gwasvcf do_coloc do_mr drug_target_evidence extract_matched_regions file_to_gwasvcf forest_plot harmonise mr_pipeline pairwise_analysis read_exposure read_outcome regional_plot volcano_plot z_comparison_plot z_plot

Dependencies:abind AnnotationDbi askpass base64enc BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome bslib cachem cigarillo cli codetools coloc cowplot cpp11 crayon crosstalk curl data.table DBI DelayedArray digest dplyr epigraphdb evaluate farver fastmap fontawesome foreach formatR fs futile.logger futile.options gassocplot generics genetics.binaRies GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glmnet glue GPArotation gridExtra gtable gwasglue gwasglue2 gwasvcf highr htmltools htmlwidgets httr ieugwasr IRanges irlba isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mime mixsqp mnormt MRMix MRPRESSO nlme openssl otel pbapply pillar pkgconfig plotly plyr png promises psych purrr R6 RadialMR rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl reshape restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo shape snow SparseArray stringi stringr SummarizedExperiment survival susieR sys tibble tidyr tidyselect tinytex TwoSampleMR UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML XVector yaml

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Help page	Topics
Calculate PVE	.calc_pve
Helper function to extract colocalisation regions for when one dataset comes from a local file and another from OpenGWAS.	.cdat_from_mixed
Splits vector into chunks	.chunk
Sub-function for the colocalisation analyses	.coloc_sub
Sub function to run SuSiE and coloc	.coloc_susie_sub
Link ENSG IDs with DGIdb	.dgidb_linkage
Convert ENSG IDs -> gene names	.ensg_to_name
Prepare gwasvcf files for coloc. This method will extract SNPs from one file using one chrompos and then look up those SNPs in the other file - this is to ensure coloc can be conducted upon two datasets of different genomic builds without the need of liftover.	.gwasvcf_to_coloc_rsid
Prepare gwasvcf files for PWCoCo	.gwasvcf_to_pwcoco
Prepare ieugwasr data for PWCoCo	.ieugwasr_to_pwcoco
IVW weighted delta	.ivw_delta
Helper function for message printing.	.print_msg
Sub-function to run PWCoCo	.pwcoco_sub
Read datasets	.read_dataset
WR Taylor Approx of SE	.wr_taylor_approx
Annotates the data using given IDs	annotate_data
Annotate diseases with EFO IDs	annotate_efo
Annotate ENSG IDs with gene names	annotate_ensg
Calculate F-statistic	calc_f_stat
Check if SNPs are good for use in analyses and mark them as such.	check_snps
Annotate cis/trans SNPs	cis_trans
Combine MR and coloc results into one data.frame	combine_results
Convert data.frame to gwasvcf format.	dat_to_gwasvcf
Run colocalisation analyses	do_coloc
Run Mendelian randomisation analyses	do_mr
Generate drug target evidence	drug_target_evidence
Extract SNPs based on region for colocalisation analyses. Can be used before calling the `do_coloc` function or will be called as part of that function automatically.	extract_matched_regions
Convert file(s) to gwasvcf format.	file_to_gwasvcf
Forest plot	forest_plot
Get column names from agnostic but formatted data.frame	get_col_name
Harmonise exposure and outcomes.	harmonise
Hello, World!	hello
Check if SNP frequencies are ambiguous	is_ambiguous
Check if SNP is palindromic	is_palindromic
Entry point for the pipeline.	mr_pipeline
Performs pairwise harmonisation and analyses - helpful when analysing many exposure-outcome pairs as performing the standard "linear" approach will be very slow.	pairwise_analysis
Read exposures	read_exposure
Read outcomes	read_outcome
Plots a regional plot of the area being tested for colocalisation	regional_plot
Validates parameters in config file	validate_config
Volcano plot	volcano_plot
Z score comparison plot	z_comparison_plot
Z plot	z_plot

Package: mrpipeline 0.1.0

mrpipeline: Implements a Ready-for-Use Mendelian Randomisation Pipeline

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