# Integrated Framework to Annotate Genetic Variants

## Documentation for package ‘annovarR’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

annovarR-package | The 'annovarR' package provides R functions as well as database resources which offer an integrated framework to annotate genetic variants from genome and transcriptome data. The wrapper functions of 'annovarR' unified the interface of many published annotation tools, such as 'VEP' (<URL: http://asia.ensembl.org/info/docs/tools/vep/index.html>), 'ANNOVAR' (<URL: http://annovar.openbioinformatics.org/>), 'vcfanno' (<URL: https://github.com/brentp/vcfanno>) and 'AnnotationDbi' (<URL: http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi.html>). It also simplified the use of some of the external annotation tools in R. Besides, massive published genetic variants annotation databases were integrated into 'annovarR'. For example, 'annovarR' provides a newly RNA-seq allele frequency database, BRVar, which built from total 1,285 cases public B-progenitor acute lymphoblastic leukemia (B-ALL) transcriptome data.
annotation | Annotation function (single name)
annotation.cols.match | A position annotation utils that can be used to write a yourself annotation function
annotation.merge | Annotation function (mulitple name)
annotation.region.match | A regeion annotation utils that can be used to write a yourself annotation function
annovar | R function to run ANNOVAR.
annovarR | The 'annovarR' package provides R functions as well as database resources which offer an integrated framework to annotate genetic variants from genome and transcriptome data. The wrapper functions of 'annovarR' unified the interface of many published annotation tools, such as 'VEP' (<URL: http://asia.ensembl.org/info/docs/tools/vep/index.html>), 'ANNOVAR' (<URL: http://annovar.openbioinformatics.org/>), 'vcfanno' (<URL: https://github.com/brentp/vcfanno>) and 'AnnotationDbi' (<URL: http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi.html>). It also simplified the use of some of the external annotation tools in R. Besides, massive published genetic variants annotation databases were integrated into 'annovarR'. For example, 'annovarR' provides a newly RNA-seq allele frequency database, BRVar, which built from total 1,285 cases public B-progenitor acute lymphoblastic leukemia (B-ALL) transcriptome data.
del | Delete table or database (text file, sqlite, mysql)
download.database | Download annovarR databases
drop.mysql.index | Drop search index of annovarR database table in mysql
drop.sqlite.index | Drop search index of annovarR database table in sqlite
get.annotation.dbtype | Get annovarR default databases type [sqlite, txt]
get.annotation.names | Get all annovarR supported databases
get.annotation.needcols | Get annovarR annotation needed colnames according the anno.name
get.download.name | Use annotation name to get download.name that can be used to download the database use 'download.database'
mysql.auto.build | Build annovarR database in mysql (auto from extdata/config/database.toml)
mysql.auto.index | Index annovarR database in mysql (auto from extdata/config/database.toml)
mysql.build | Build annovarR database in mysql
mysql.head | Show top n line of table of database in mysql database
mysql.index | Generate search index of annovarR database table in mysql
mysql.tb.colnames | Get colnames of table of database in mysql
mysql.tb.indexes | Get mysql table indexes
sql2sqlite | Convert sql file to sqlite database
sqlite.auto.build | Build annovarR database in sqlite (auto from extdata/config/database.toml)
sqlite.auto.index | Index annovarR database in sqlite (auto from extdata/config/database.toml)
sqlite.build | Build annovarR database in sqlite
sqlite.head | Show top n line of table of database in sqlite database
sqlite.index | Generate search index of annovarR database table in sqlite
sqlite.tb.colnames | Get colnames of table of database in sqlite
sqlite.tb.indexes | Get sqlite table indexes
sqlite2sql | Function to dump sqlite database (Now only use system version sqlite)
vcfanno | R function to run vcfanno
vep | R function to run VEP