\documentclass[12pt]{article}
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\title{MyVariant.info R Client}
\author{Adam Mark, Chunlei Wu}

\begin{document}
\SweaveOpts{concordance=TRUE}

\maketitle

\tableofcontents

\section{Overview}

MyVariant.Info is a simple-to-use REST web service to query/retrieve genetic variant annotation from an aggregation of variant annotation resources. \Rpackage{myvariant} is an easy-to-use R wrapper to access MyVariant.Info services and explore variant annotions.
\section{Variant Annotation Service}

\subsection{Obtaining HGVS IDs from a VCF file. }

\begin{itemize}
\item Use \Rfunction{readVcf} from the VariantAnnotation package to read a Vcf file in. The Vcf object can then be passed to \Rfunction{formatHgvs} to retrieve HGVS IDs. HGVS IDs are based on the GRCh38/hg19 reference genome. Support for hg38 is coming soon.
\end{itemize} 

<<echo=FALSE>>=
library(myvariant)
library(VariantAnnotation)
@

<<>>=
file.path <- system.file("extdata", "dbsnp_mini.vcf", package="myvariant")
vcf <- readVcf(file.path, genome="hg19")
rowRanges(vcf)
@ 
\begin{itemize}
\item You can then use \Rfunction{formatHgvs} to extract HGVS IDs from the Vcf object.
\end{itemize}

<<>>=
hgvs <- formatHgvs(vcf, variant_type="snp")
head(hgvs)
@


\subsection{\Rfunction{getVariant}}

\begin{itemize}
\item Use \Rfunction{getVariant}, the wrapper for GET query of "/v1/variant/<hgvsid>" service, to return the variant object for the given HGVS id.
\end{itemize} 


<<>>=
variant <- getVariant("chr1:g.35367G>A")
variant[[1]]$dbnsfp$genename
variant[[1]]$cadd$phred
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\subsection{\Rfunction{getVariants}}

\begin{itemize}
\item Use \Rfunction{getVariants}, the wrapper for POST query of "/v1/variant" service, to return the list of variant objects for the given character vector of HGVS ids.
\end{itemize} 


<<>>=
getVariants(c("chr1:g.35367G>A", "chr16:g.28883241A>G"),
            fields="cadd.consequence")
@


\section{Variant Query Service}

\subsection{\Rfunction{queryVariant}}

\begin{itemize}
\item \Rfunction{queryVariant} is a wrapper for GET query of "/v1/query?q=<query>" service, to return  the query result. This function accepts wild card input terms and allows you to query for variants that contain a specific annotation. For example, the following query searches for the CADD phred score and consequence for all variants whose genename (dbNSFP) is MLL2.
\end{itemize}



<<>>=
queryVariant(q="dbnsfp.genename:MLL2", fields=c("cadd.phred", "cadd.consequence"))
@

\begin{itemize}
\item You can also use \Rfunction{queryVariant} to retrieve all annotations that map to a specific rsID.
\end{itemize}

<<>>=
queryVariant(q="rs58991260", fields="dbsnp.flags")$hits
@

\subsection{\Rfunction{queryVariants}}

\begin{itemize}
\item \Rfunction{queryVariants} is a wrapper for POST query of "/v1/query?q=<query>" service, to return  the query result. Query terms include any available field as long as scopes are defined. The following example reads the dbSNP rsIDs from a VCF and queries for all fields. The returned DataFrame can then be easily subsetted to include, for example, those that have not been documented in the Wellderly study.
\end{itemize}


<<>>=
rsids <- paste("rs", info(vcf)$RS, sep="")
res <- queryVariants(q=rsids, scopes="dbsnp.rsid", fields="all")
subset(res, !is.na(wellderly.vartype))$query
@




\section{References}
MyVariant.info
help@myvariant.info

\end{document}