Abstract
We developed haploR, an R package for querying web based genome annotation tools HaploReg and RegulomeDB. haploR gathers information in a data frame which is suitable for downstream bioinformatic analyses. This will facilitate post-genome wide association studies streamline analysis for rapid discovery and interpretation of genetic associations.
Highlights
Genomic experiments, including genome wide association studies (GWAS), produced and continue to produce a huge amount of data
There exists a set of web-based tools, such as HaploReg[2] and RegulomeDB3, which offer a link of detected genetic variants to additional post-GWAS information
We present an R-package, haploR, which allows for querying HaploReg and RegulomeDB web-based tools
Summary
Genomic experiments, including genome wide association studies (GWAS), produced and continue to produce a huge amount of data. To better understand the biological mechanisms involved in regulation complex traits, this information requires further analysis Large projects, such as ENCODE1, are devoted to bring together accumulated knowledge about different functional and regulatory elements that control cells’ functioning. There exists a set of web-based tools, such as HaploReg[2] and RegulomeDB3, which offer a link of detected genetic variants to additional post-GWAS information These include information about linkage disequilibrium (LD), expression quantitative trait loci (eQTL), allele frequencies, protein functions, chromatin states, etc., for annotated genetic variants. These tools are webbased, which requires the user to open a web page, manually enter information and obtain the results of such linking in a certain format.
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