postgwas-package: GWAS post-processing utilities
In merns/postgwas: GWAS Post-Processing Utilities
Description
Annotate genes to SNPs (using proximity or LD information), see snp2gene
Create regional and manhattan plots
Interaction network analysis of GWAS data, see gwas2network
search literature (under development)
Details
This package contains several functions that are designed to simplify the interpretation of genomewide association studies (GWAS).
Firstly, some frequently used visualization tools are implemented here in R that provide plots of publication-ready quality (manhattanplot, regionalplot). The manhattan plotting function offers highlighting features and the regional plots display genes, exons, p-values from multiple GWAS result files (comparative plot),linkage disequilibrium and SNP numbers upon users choice from diverse formats and data sources. There are options for additional rare variant track. Regional plots can be produced for many loci at once in a single pdf or png file. There is a function for comprehensive interaction network analysis of GWAS results, including download and construction of networks (gwas2network, getInteractions).
All these functions can be run in a line with default parameters using the postgwas function, but it is recommended to use the individual functions for high-quality results.
Contributions to the package (additional functions, code extensions, bugfixed, suggestions for parameter changes etc) are much appreciated (please contact the package maintainer by mail).
Author(s)
Milan Hiersche <mihi@uni-muenster.de>
merns/postgwas documentation built on May 22, 2019, 6:53 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description
Annotate genes to SNPs (using proximity or LD information), see
snp2geneCreate
regionalandmanhattanplotsInteraction network analysis of GWAS data, see
gwas2networksearch literature (under development)
Details
This package contains several functions that are designed to simplify the interpretation of genomewide association studies (GWAS). Firstly, some frequently used visualization tools are implemented here in R that provide plots of publication-ready quality (manhattanplot, regionalplot). The manhattan plotting function offers highlighting features and the regional plots display genes, exons, p-values from multiple GWAS result files (comparative plot),linkage disequilibrium and SNP numbers upon users choice from diverse formats and data sources. There are options for additional rare variant track. Regional plots can be produced for many loci at once in a single pdf or png file. There is a function for comprehensive interaction network analysis of GWAS results, including download and construction of networks (gwas2network, getInteractions).
All these functions can be run in a line with default parameters using the postgwas function, but it is recommended to use the individual functions for high-quality results.
Contributions to the package (additional functions, code extensions, bugfixed, suggestions for parameter changes etc) are much appreciated (please contact the package maintainer by mail).
Author(s)
Milan Hiersche <mihi@uni-muenster.de>
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.