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Package: locuscomparer 1.0.0

Boxiang Liu

locuscomparer: locuscomparer: Visualization of GWAS-QTL Colocalization Events

locuscomparer is the standalone version of the LocusCompare webserver (www.locuscompare.ml:3838). locuscomparer performs visualization of colocalization of summary statistics from pairs of association datasets (e.g. GWAS and eQTL).

Authors:Boxiang Liu [aut, cre], Michael Gloudemans [ctb], Stephen Montgomery [ctb]

locuscomparer_1.0.0.tar.gz
locuscomparer_1.0.0.zip(r-4.7)locuscomparer_1.0.0.zip(r-4.6)locuscomparer_1.0.0.zip(r-4.5)
locuscomparer_1.0.0.tgz(r-4.6-any)locuscomparer_1.0.0.tgz(r-4.5-any)
locuscomparer_1.0.0.tar.gz(r-4.7-any)locuscomparer_1.0.0.tar.gz(r-4.6-any)
locuscomparer_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
locuscomparer/json (API)
NEWS

# Install 'locuscomparer' in R:

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

Bug tracker:https://github.com/remlapmot/locuscomparer/issues

Datasets:

config - Example dataset

On CRAN:

2.80 score 125 scripts 10 exports 22 dependencies

Last updated from:208d7fae39 (on suggestions). Checks:7 ERROR, 2 OK. Indexed: no.

Target	Result	Time
linux-devel-x86_64	ERROR	143
source / vignettes	OK	132
linux-release-x86_64	ERROR	133
macos-release-arm64	ERROR	105
macos-oldrel-arm64	ERROR	140
windows-devel	ERROR	97
windows-release	ERROR	76
windows-oldrel	ERROR	69
wasm-release	OK	108

Exports:add_label assign_color get_lead_snp get_position locuscompare make_combined_plot make_locuszoom make_scatterplot read_metal retrieve_LD

Dependencies:cli cowplot cpp11 DBI farver ggplot2 ggrepel glue gtable isoband labeling lifecycle R6 RColorBrewer Rcpp rlang RMySQL S7 scales vctrs viridisLite withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add a column of SNP labels to input data.frame	add_label
Assign color to each SNP according to LD.	assign_color
Example dataset	config
Get the lead SNP from the list of SNPs in input data.frame The lead SNP is defined as the SNP with the lowest sum of p-values from the two studies.	get_lead_snp
Append two columns, chromosome (chr) and position (pos), to the input data.frame.	get_position
Make a locuscompare plot.	locuscompare
Generated a combined plot with two locuszoom plots and a locuscompare plot. Each locuszoom plot represent an association study.	make_combined_plot
Make a locuszoom plot. Details see http://locuszoom.org/.	make_locuszoom
Make a scatter plot (called the LocusCompare plot). Each axis of the LocusCompare plot represent the -log10(p-value) from an association study. Each point thus represent a SNP. By default, the lead SNP is a purple diamond, whereas the other SNPs are colored according to their LD with the lead SNP.	make_scatterplot
Read association summary statistics from file and append column. The file must contain 2 columns: markers, i.e SNPs, and p-value. The marker column should contain SNP rsIDs.	read_metal
Retrive SNP pairwise LD from database. SNP pairwise lD are calculated based on 1000 Genomes Project Phase 3 version 5. For storage-efficiency, the output will only include SNPs with r2 > 0.2 with the input SNP.	retrieve_LD