annotation.cols.match: A position annotation utils that can be used to write a...
In annovarR: Integrated Framework to Annotate Genetic Variants

A position annotation utils that can be used to write a yourself annotation function

annotation.cols.match(dat = data.table(), anno.name = "",
  buildver = "hg19", database.dir = Sys.getenv("annovarR_DB_DIR", ""),
  db.col.order = 1:5, index.cols = c("chr", "start"),
  matched.cols = c("chr", "start", "end", "ref", "alt"),
  return.col.index = 6, return.col.names = "",
  return.col.names.profix = "", format.dat.fun = format.cols,
  dbname.fixed = NULL, table.name.fixed = NULL, setdb.fun = set.db,
  set.table.fun = set.table, format.db.tb.fun = format.db.tb,
  db.type = "sqlite", db.file.prefix = NULL,
  mysql.connect.params = list(), sqlite.connect.params = list(),
  fread.db.params = list(), verbose = FALSE)

`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
`buildver`	Genome version, hg19, hg38, mm10 and others
`database.dir`	Dir of the databases (mysql no need)
`db.col.order`	Using the index, you can rename the database table, and can be matched using matched.cols.
`index.cols`	Using the selected cols to match data with sqlite database. eg. c('chr', 'start'), 'rs'
`matched.cols`	Using the selected cols to match data with selected partial data by index.cols limited.
`return.col.index`	Setting the colnums need be returned
`return.col.names`	Setting the returned colnum names
`return.col.names.profix`	Setting the returned colnum names profix
`format.dat.fun`	A function to process input data. eg. as.numeric(dat$start); as.character(dat$chr)
`dbname.fixed`	Database path (txt, sqlite) or name (MySQL), default is NULL, and get from setdb.fun (Set value will fix the dbname, and will be added in sqlite.connenct.params and mysql.connect.params)
`table.name.fixed`	Table name, default is NULL, and get from set.table.fun (Set value will fix the table.name) (Set value will fix the table.name, and will be added in sqlite.connenct.params and mysql.connect.params)
`setdb.fun`	A function to process the name, buildver, database.dir and get the database path (MySQL return NULL)
`set.table.fun`	A function to process the name, buildver and get the final table name
`format.db.tb.fun`	A function to process the selected database table that can be used to matched with your data
`db.type`	Setting the database type (sqlite, txt or mysql)
`db.file.prefix`	Only be setted when db.type is local databae like sqlite or txt
`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
`fread.db.params`	For text format database, you can use fread.db.params to control the fread behavior
`verbose`	Logical indicating wheather print the extra log infomation

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.cols.match(dat, 'avsnp147', database.dir = database.dir, 
return.col.names = 'avSNP147', db.type = 'txt')