All functions

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' (http://asia.ensembl.org/info/docs/tools/vep/index.html), 'ANNOVAR' (http://annovar.openbioinformatics.org/), 'vcfanno' (https://github.com/brentp/vcfanno) and 'AnnotationDbi' (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.

check_shiny_dep()

Function to check dependence package running annovarR shiny app

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

set_shiny_workers()

Function to set shiny workers for background service

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

web()

Function to run annovarR shiny APP service