annovarR (version 1.0.0)

annotation: Annotation function (single name)

Description

Annotation function (single name)

Usage

annotation(dat = data.table(), anno.name = "", buildver = "hg19",
  annovar.anno.names = "", database.dir = Sys.getenv("annovarR_DB_DIR", ""),
  db.type = NULL, database.cfg = system.file("extdata",
  "config/databases.toml", package = "annovarR"), func = NULL,
  mysql.connect.params = list(host = "", dbname = "", table.name = "", user =
  "", password = ""), sqlite.connect.params = list(dbname = ""), ...)

Arguments

dat

A data.table including all of your data, eg. data.table(chr=c(1,2,3), start=c(1111,1112,1113))

anno.name

Annotation name, eg. avsnp138, avsnp147, 1000g2015aug_all .etc.

buildver

Genome version, hg19, hg38, mm10 and others

annovar.anno.names

If anno.name equal perl_annovar_merge, you can use annovar.anno.names to annotate multiple database supported by ANNOVAR, the names can be found on the http://annovar.openbioinformatics.org/en/latest/user-guide/download/

database.dir

Dir of the databases

db.type

Setting the database type (sqlite or txt)

database.cfg

Configuration file of annovarR databases infomation

func

Function to anntate the dat data, default is to search the function in extdata/database.toml

mysql.connect.params

Connect MySQL database other parameters, e.g. list(host='11.11.11.1', port = '3306', user = '', password = '123456')

sqlite.connect.params

Connect SqLite database other paramertes, default is not need

...

Other parameters see annotation.cols.match, annotation.region.match, annovar and vep

Examples

# NOT RUN {
library(data.table)
chr <- c('chr1', 'chr2', 'chr1')
start <- c('10020', '10020', '10020')
end <- c('10020', '10020', '10020')
ref <- c('A', 'A', 'A')
alt <- c('-', '-', '-')
database <- system.file('extdata', 'demo/hg19_avsnp147.txt', package = 'annovarR')
database.dir <- dirname(database)
dat <- data.table(chr = chr, start = start, end = end, ref = ref, alt = alt)
x <- annotation(dat, 'avsnp147', database.dir = database.dir, 
return.col.names = 'avSNP147', db.type = 'txt')
# }