Man pages for annovarR
Integrated Framework to Annotate Genetic Variants
| annotation | Annotation function (single name) |
| annotation.cols.match | A position annotation utils that can be used to write a... |
| annotation.merge | Annotation function (mulitple name) |
| annotation.region.match | A regeion annotation utils that can be used to write a... |
| annovar | R function to run ANNOVAR. |
| annovarR | The 'annovarR' package provides R functions as well as... |
| 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... |
| get.download.name | Use annotation name to get download.name that can be used to... |
| mysql.auto.build | Build annovarR database in mysql (auto from... |
| mysql.auto.index | Index annovarR database in mysql (auto from... |
| 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 |
| sqlite2sql | Function to dump sqlite database (Now only use system version... |
| sqlite.auto.build | Build annovarR database in sqlite (auto from... |
| sqlite.auto.index | Index annovarR database in sqlite (auto from... |
| 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 |
| vcfanno | R function to run vcfanno |
| vep | R function to run VEP |
