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LocusCompareR

1. Installation

LocusCompareR is an R package for visualization of GWAS-eQTL colocalization events.

Use the following commands to install LocusCompareR. If you don't have devtools, uncomment the first line to install it.

# install.packages("devtools")
devtools::install_github("boxiangliu/locuscomparer")

2. Example

To illustrate the use of locuscompare, we use the GWAS dataset from Nikpay et al. (2015) and the coronary artery eQTL dataset from GTEx v7 at the PHACTR1 locus:

library(locuscomparer)
gwas_fn = system.file('extdata','gwas.tsv', package = 'locuscomparer')
eqtl_fn = system.file('extdata','eqtl.tsv', package = 'locuscomparer')
locuscompare(in_fn1 = gwas_fn, in_fn2 = eqtl_fn, title1 = 'CAD GWAS', title2 = 'Coronary Artery eQTL')

The output from the main function is a figure like the following:

The labeled SNP is the lead SNP (in this case for both studies), and other SNPs are colored according to their LD $r^2$ with the lead SNP.

3. Using your own dataset:

The input to locuscompare::main() is a two-column tab-delimited text file with two columns:

  1. rsid
  2. pval

Here is an example file:

rsid	pval
rs62156064	0.564395
rs7562234	0.399642
rs11677377	0.34308
rs35076156	0.625237

You can download the example files below: GWAS and eQTL datasets.

Then run the following commands:

library(locuscomparer)
gwas_fn = 'path/to/gwas.tsv'
eqtl_fn = 'path/to/eqtl.tsv'
locuscompare(in_fn1 = gwas_fn, in_fn2 = eqtl_fn, title = 'GWAS', title2 = 'eQTL')

4. Documentations

To view documentation for each function, type ?[function name] in the R console.

LocusCompareR current export the following functions:

Data munging

  • assign_color: Assign color to each SNP according to LD.
  • get_lead_snp: Add a column of SNP labels to input data.frame.
  • get_position: Append two columns, chromosome (chr) and position (pos), to the input data.frame.

Plotting

  • locuscompare: Make a locuscompare plot.
  • make_combined_plot: Generated a combined plot with two locuszoom plots and a locuscompare plot.
  • make_locuszoom: Make a simple locuszoom plot.
  • make_scatterplot: Make a scatter plot (called the LocusCompare plot)

Data loading

  • read_metal" Read association summary statistics from file.
  • retrieve_LD: Retrive SNP pairwise LD from database.

About

LocusCompareR is a R package with visualization tools for comparing two genetic association datasets.

Resources

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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LocusCompareR
1. Installation
LocusCompareR is an R package for visualization of GWAS-eQTL colocalization events.
Use the following commands to install LocusCompareR. If you don't have devtools, uncomment the first line to install it.
# install.packages("devtools")
devtools::install_github("boxiangliu/locuscomparer")

2. Example
To illustrate the use of locuscompare, we use the GWAS dataset from Nikpay et al. (2015) and the coronary artery eQTL dataset from GTEx v7 at the PHACTR1 locus:
library(locuscomparer)
gwas_fn = system.file('extdata','gwas.tsv', package = 'locuscomparer')
eqtl_fn = system.file('extdata','eqtl.tsv', package = 'locuscomparer')
locuscompare(in_fn1 = gwas_fn, in_fn2 = eqtl_fn, title1 = 'CAD GWAS', title2 = 'Coronary Artery eQTL')

The output from the main function is a figure like the following:
The labeled SNP is the lead SNP (in this case for both studies), and other SNPs are colored according to their LD $r^2$ with the lead SNP.
3. Using your own dataset:
The input to locuscompare::main() is a two-column tab-delimited text file with two columns:
  1. rsid
  2. pval
Here is an example file:
rsid	pval
rs62156064	0.564395
rs7562234	0.399642
rs11677377	0.34308
rs35076156	0.625237

You can download the example files below: GWAS and eQTL datasets.
Then run the following commands:
library(locuscomparer)
gwas_fn = 'path/to/gwas.tsv'
eqtl_fn = 'path/to/eqtl.tsv'
locuscompare(in_fn1 = gwas_fn, in_fn2 = eqtl_fn, title = 'GWAS', title2 = 'eQTL')

4. Documentations
To view documentation for each function, type ?[function name] in the R console.
LocusCompareR current export the following functions:
Data munging
  • assign_color: Assign color to each SNP according to LD.
  • get_lead_snp: Add a column of SNP labels to input data.frame.
  • get_position: Append two columns, chromosome (chr) and position (pos), to the input data.frame.
Plotting
  • locuscompare: Make a locuscompare plot.
  • make_combined_plot: Generated a combined plot with two locuszoom plots and a locuscompare plot.
  • make_locuszoom: Make a simple locuszoom plot.
  • make_scatterplot: Make a scatter plot (called the LocusCompare plot)
Data loading
  • read_metal" Read association summary statistics from file.
  • retrieve_LD: Retrive SNP pairwise LD from database.
About
LocusCompareR is a R package with visualization tools for comparing two genetic association datasets.
Resources
Readme
Activity
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, 'i');
if (__m === '*' || __re.test(location.href)) {
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})();
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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LocusCompareR
1. Installation
LocusCompareR is an R package for visualization of GWAS-eQTL colocalization events.
Use the following commands to install LocusCompareR. If you don't have devtools, uncomment the first line to install it.
# install.packages("devtools")
devtools::install_github("boxiangliu/locuscomparer")

2. Example
To illustrate the use of locuscompare, we use the GWAS dataset from Nikpay et al. (2015) and the coronary artery eQTL dataset from GTEx v7 at the PHACTR1 locus:
library(locuscomparer)
gwas_fn = system.file('extdata','gwas.tsv', package = 'locuscomparer')
eqtl_fn = system.file('extdata','eqtl.tsv', package = 'locuscomparer')
locuscompare(in_fn1 = gwas_fn, in_fn2 = eqtl_fn, title1 = 'CAD GWAS', title2 = 'Coronary Artery eQTL')

The output from the main function is a figure like the following:
The labeled SNP is the lead SNP (in this case for both studies), and other SNPs are colored according to their LD $r^2$ with the lead SNP.
3. Using your own dataset:
The input to locuscompare::main() is a two-column tab-delimited text file with two columns:
  1. rsid
  2. pval
Here is an example file:
rsid	pval
rs62156064	0.564395
rs7562234	0.399642
rs11677377	0.34308
rs35076156	0.625237

You can download the example files below: GWAS and eQTL datasets.
Then run the following commands:
library(locuscomparer)
gwas_fn = 'path/to/gwas.tsv'
eqtl_fn = 'path/to/eqtl.tsv'
locuscompare(in_fn1 = gwas_fn, in_fn2 = eqtl_fn, title = 'GWAS', title2 = 'eQTL')

4. Documentations
To view documentation for each function, type ?[function name] in the R console.
LocusCompareR current export the following functions:
Data munging
  • assign_color: Assign color to each SNP according to LD.
  • get_lead_snp: Add a column of SNP labels to input data.frame.
  • get_position: Append two columns, chromosome (chr) and position (pos), to the input data.frame.
Plotting
  • locuscompare: Make a locuscompare plot.
  • make_combined_plot: Generated a combined plot with two locuszoom plots and a locuscompare plot.
  • make_locuszoom: Make a simple locuszoom plot.
  • make_scatterplot: Make a scatter plot (called the LocusCompare plot)
Data loading
  • read_metal" Read association summary statistics from file.
  • retrieve_LD: Retrive SNP pairwise LD from database.
About
LocusCompareR is a R package with visualization tools for comparing two genetic association datasets.
Resources
Readme
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
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} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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LocusCompareR
1. Installation
LocusCompareR is an R package for visualization of GWAS-eQTL colocalization events.
Use the following commands to install LocusCompareR. If you don't have devtools, uncomment the first line to install it.
# install.packages("devtools")
devtools::install_github("boxiangliu/locuscomparer")

2. Example
To illustrate the use of locuscompare, we use the GWAS dataset from Nikpay et al. (2015) and the coronary artery eQTL dataset from GTEx v7 at the PHACTR1 locus:
library(locuscomparer)
gwas_fn = system.file('extdata','gwas.tsv', package = 'locuscomparer')
eqtl_fn = system.file('extdata','eqtl.tsv', package = 'locuscomparer')
locuscompare(in_fn1 = gwas_fn, in_fn2 = eqtl_fn, title1 = 'CAD GWAS', title2 = 'Coronary Artery eQTL')

The output from the main function is a figure like the following:
The labeled SNP is the lead SNP (in this case for both studies), and other SNPs are colored according to their LD $r^2$ with the lead SNP.
3. Using your own dataset:
The input to locuscompare::main() is a two-column tab-delimited text file with two columns:
  1. rsid
  2. pval
Here is an example file:
rsid	pval
rs62156064	0.564395
rs7562234	0.399642
rs11677377	0.34308
rs35076156	0.625237

You can download the example files below: GWAS and eQTL datasets.
Then run the following commands:
library(locuscomparer)
gwas_fn = 'path/to/gwas.tsv'
eqtl_fn = 'path/to/eqtl.tsv'
locuscompare(in_fn1 = gwas_fn, in_fn2 = eqtl_fn, title = 'GWAS', title2 = 'eQTL')

4. Documentations
To view documentation for each function, type ?[function name] in the R console.
LocusCompareR current export the following functions:
Data munging
  • assign_color: Assign color to each SNP according to LD.
  • get_lead_snp: Add a column of SNP labels to input data.frame.
  • get_position: Append two columns, chromosome (chr) and position (pos), to the input data.frame.
Plotting
  • locuscompare: Make a locuscompare plot.
  • make_combined_plot: Generated a combined plot with two locuszoom plots and a locuscompare plot.
  • make_locuszoom: Make a simple locuszoom plot.
  • make_scatterplot: Make a scatter plot (called the LocusCompare plot)
Data loading
  • read_metal" Read association summary statistics from file.
  • retrieve_LD: Retrive SNP pairwise LD from database.
About
LocusCompareR is a R package with visualization tools for comparing two genetic association datasets.
Resources
Readme
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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LocusCompareR
1. Installation
LocusCompareR is an R package for visualization of GWAS-eQTL colocalization events.
Use the following commands to install LocusCompareR. If you don't have devtools, uncomment the first line to install it.
# install.packages("devtools")
devtools::install_github("boxiangliu/locuscomparer")

2. Example
To illustrate the use of locuscompare, we use the GWAS dataset from Nikpay et al. (2015) and the coronary artery eQTL dataset from GTEx v7 at the PHACTR1 locus:
library(locuscomparer)
gwas_fn = system.file('extdata','gwas.tsv', package = 'locuscomparer')
eqtl_fn = system.file('extdata','eqtl.tsv', package = 'locuscomparer')
locuscompare(in_fn1 = gwas_fn, in_fn2 = eqtl_fn, title1 = 'CAD GWAS', title2 = 'Coronary Artery eQTL')

The output from the main function is a figure like the following:
The labeled SNP is the lead SNP (in this case for both studies), and other SNPs are colored according to their LD $r^2$ with the lead SNP.
3. Using your own dataset:
The input to locuscompare::main() is a two-column tab-delimited text file with two columns:
  1. rsid
  2. pval
Here is an example file:
rsid	pval
rs62156064	0.564395
rs7562234	0.399642
rs11677377	0.34308
rs35076156	0.625237

You can download the example files below: GWAS and eQTL datasets.
Then run the following commands:
library(locuscomparer)
gwas_fn = 'path/to/gwas.tsv'
eqtl_fn = 'path/to/eqtl.tsv'
locuscompare(in_fn1 = gwas_fn, in_fn2 = eqtl_fn, title = 'GWAS', title2 = 'eQTL')

4. Documentations
To view documentation for each function, type ?[function name] in the R console.
LocusCompareR current export the following functions:
Data munging
  • assign_color: Assign color to each SNP according to LD.
  • get_lead_snp: Add a column of SNP labels to input data.frame.
  • get_position: Append two columns, chromosome (chr) and position (pos), to the input data.frame.
Plotting
  • locuscompare: Make a locuscompare plot.
  • make_combined_plot: Generated a combined plot with two locuszoom plots and a locuscompare plot.
  • make_locuszoom: Make a simple locuszoom plot.
  • make_scatterplot: Make a scatter plot (called the LocusCompare plot)
Data loading
  • read_metal" Read association summary statistics from file.
  • retrieve_LD: Retrive SNP pairwise LD from database.
About
LocusCompareR is a R package with visualization tools for comparing two genetic association datasets.
Resources
Readme
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
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Packages
Contributors
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
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} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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LocusCompareR
1. Installation
LocusCompareR is an R package for visualization of GWAS-eQTL colocalization events.
Use the following commands to install LocusCompareR. If you don't have devtools, uncomment the first line to install it.
# install.packages("devtools")
devtools::install_github("boxiangliu/locuscomparer")

2. Example
To illustrate the use of locuscompare, we use the GWAS dataset from Nikpay et al. (2015) and the coronary artery eQTL dataset from GTEx v7 at the PHACTR1 locus:
library(locuscomparer)
gwas_fn = system.file('extdata','gwas.tsv', package = 'locuscomparer')
eqtl_fn = system.file('extdata','eqtl.tsv', package = 'locuscomparer')
locuscompare(in_fn1 = gwas_fn, in_fn2 = eqtl_fn, title1 = 'CAD GWAS', title2 = 'Coronary Artery eQTL')

The output from the main function is a figure like the following:
The labeled SNP is the lead SNP (in this case for both studies), and other SNPs are colored according to their LD $r^2$ with the lead SNP.
3. Using your own dataset:
The input to locuscompare::main() is a two-column tab-delimited text file with two columns:
  1. rsid
  2. pval
Here is an example file:
rsid	pval
rs62156064	0.564395
rs7562234	0.399642
rs11677377	0.34308
rs35076156	0.625237

You can download the example files below: GWAS and eQTL datasets.
Then run the following commands:
library(locuscomparer)
gwas_fn = 'path/to/gwas.tsv'
eqtl_fn = 'path/to/eqtl.tsv'
locuscompare(in_fn1 = gwas_fn, in_fn2 = eqtl_fn, title = 'GWAS', title2 = 'eQTL')

4. Documentations
To view documentation for each function, type ?[function name] in the R console.
LocusCompareR current export the following functions:
Data munging
  • assign_color: Assign color to each SNP according to LD.
  • get_lead_snp: Add a column of SNP labels to input data.frame.
  • get_position: Append two columns, chromosome (chr) and position (pos), to the input data.frame.
Plotting
  • locuscompare: Make a locuscompare plot.
  • make_combined_plot: Generated a combined plot with two locuszoom plots and a locuscompare plot.
  • make_locuszoom: Make a simple locuszoom plot.
  • make_scatterplot: Make a scatter plot (called the LocusCompare plot)
Data loading
  • read_metal" Read association summary statistics from file.
  • retrieve_LD: Retrive SNP pairwise LD from database.
About
LocusCompareR is a R package with visualization tools for comparing two genetic association datasets.
Resources
Readme
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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LocusCompareR
1. Installation
LocusCompareR is an R package for visualization of GWAS-eQTL colocalization events.
Use the following commands to install LocusCompareR. If you don't have devtools, uncomment the first line to install it.
# install.packages("devtools")
devtools::install_github("boxiangliu/locuscomparer")

2. Example
To illustrate the use of locuscompare, we use the GWAS dataset from Nikpay et al. (2015) and the coronary artery eQTL dataset from GTEx v7 at the PHACTR1 locus:
library(locuscomparer)
gwas_fn = system.file('extdata','gwas.tsv', package = 'locuscomparer')
eqtl_fn = system.file('extdata','eqtl.tsv', package = 'locuscomparer')
locuscompare(in_fn1 = gwas_fn, in_fn2 = eqtl_fn, title1 = 'CAD GWAS', title2 = 'Coronary Artery eQTL')

The output from the main function is a figure like the following:
The labeled SNP is the lead SNP (in this case for both studies), and other SNPs are colored according to their LD $r^2$ with the lead SNP.
3. Using your own dataset:
The input to locuscompare::main() is a two-column tab-delimited text file with two columns:
  1. rsid
  2. pval
Here is an example file:
rsid	pval
rs62156064	0.564395
rs7562234	0.399642
rs11677377	0.34308
rs35076156	0.625237

You can download the example files below: GWAS and eQTL datasets.
Then run the following commands:
library(locuscomparer)
gwas_fn = 'path/to/gwas.tsv'
eqtl_fn = 'path/to/eqtl.tsv'
locuscompare(in_fn1 = gwas_fn, in_fn2 = eqtl_fn, title = 'GWAS', title2 = 'eQTL')

4. Documentations
To view documentation for each function, type ?[function name] in the R console.
LocusCompareR current export the following functions:
Data munging
  • assign_color: Assign color to each SNP according to LD.
  • get_lead_snp: Add a column of SNP labels to input data.frame.
  • get_position: Append two columns, chromosome (chr) and position (pos), to the input data.frame.
Plotting
  • locuscompare: Make a locuscompare plot.
  • make_combined_plot: Generated a combined plot with two locuszoom plots and a locuscompare plot.
  • make_locuszoom: Make a simple locuszoom plot.
  • make_scatterplot: Make a scatter plot (called the LocusCompare plot)
Data loading
  • read_metal" Read association summary statistics from file.
  • retrieve_LD: Retrive SNP pairwise LD from database.
About
LocusCompareR is a R package with visualization tools for comparing two genetic association datasets.
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LocusCompareR
1. Installation
LocusCompareR is an R package for visualization of GWAS-eQTL colocalization events.
Use the following commands to install LocusCompareR. If you don't have devtools, uncomment the first line to install it.
# install.packages("devtools")
devtools::install_github("boxiangliu/locuscomparer")

2. Example
To illustrate the use of locuscompare, we use the GWAS dataset from Nikpay et al. (2015) and the coronary artery eQTL dataset from GTEx v7 at the PHACTR1 locus:
library(locuscomparer)
gwas_fn = system.file('extdata','gwas.tsv', package = 'locuscomparer')
eqtl_fn = system.file('extdata','eqtl.tsv', package = 'locuscomparer')
locuscompare(in_fn1 = gwas_fn, in_fn2 = eqtl_fn, title1 = 'CAD GWAS', title2 = 'Coronary Artery eQTL')

The output from the main function is a figure like the following:
The labeled SNP is the lead SNP (in this case for both studies), and other SNPs are colored according to their LD $r^2$ with the lead SNP.
3. Using your own dataset:
The input to locuscompare::main() is a two-column tab-delimited text file with two columns:
  1. rsid
  2. pval
Here is an example file:
rsid	pval
rs62156064	0.564395
rs7562234	0.399642
rs11677377	0.34308
rs35076156	0.625237

You can download the example files below: GWAS and eQTL datasets.
Then run the following commands:
library(locuscomparer)
gwas_fn = 'path/to/gwas.tsv'
eqtl_fn = 'path/to/eqtl.tsv'
locuscompare(in_fn1 = gwas_fn, in_fn2 = eqtl_fn, title = 'GWAS', title2 = 'eQTL')

4. Documentations
To view documentation for each function, type ?[function name] in the R console.
LocusCompareR current export the following functions:
Data munging
  • assign_color: Assign color to each SNP according to LD.
  • get_lead_snp: Add a column of SNP labels to input data.frame.
  • get_position: Append two columns, chromosome (chr) and position (pos), to the input data.frame.
Plotting
  • locuscompare: Make a locuscompare plot.
  • make_combined_plot: Generated a combined plot with two locuszoom plots and a locuscompare plot.
  • make_locuszoom: Make a simple locuszoom plot.
  • make_scatterplot: Make a scatter plot (called the LocusCompare plot)
Data loading
  • read_metal" Read association summary statistics from file.
  • retrieve_LD: Retrive SNP pairwise LD from database.
About
LocusCompareR is a R package with visualization tools for comparing two genetic association datasets.
Resources
Readme
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages