annotation: Annotation function (single name)

In JhuangLab/annovarR: Integrated Framework to Annotate Genetic Variants

Description

Annotation function (single name)

Usage

annotation(
  dat = data.table(),
  anno.name = "",
  buildver = "hg19",
  annovar.anno.names = "",
  database.dir = Sys.getenv("anor_DB_DIR", ""),
  db.type = NULL,
  database.cfg = system.file("extdata", "config/databases.toml", package = "anor"),
  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 anor 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

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 = 'anor')
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')

JhuangLab/annovarR documentation built on April 23, 2020, 10:51 p.m.