annotation.region.match: A regeion annotation utils that can be used to write a...
In JhuangLab/annovarR: Integrated Framework to Annotate Genetic Variants

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

annotation.region.match(
  dat = data.table(),
  anno.name = "",
  buildver = "hg19",
  database.dir = Sys.getenv("anor_DB_DIR", ""),
  db_col_order = 1:3,
  index_cols = c("chr", "start", "end"),
  full.matched_cols = "chr",
  inferior_col = "start",
  superior_col = "end",
  return_col_index = 4,
  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.region.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'
`full.matched_cols`	Using the selected cols to match data with selected partial data by index_cols limited.
`inferior_col`	Inferior limit col, e.g. start
`superior_col`	Superior limit col, e.g. end
`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)
bed.file <- system.file('extdata', 'demo/example.bed', package = 'anor')
bed.sqlite <- sprintf('%s/%s.sqlite', tempdir(), basename(bed.file))
connect.params <- list(dbname = bed.sqlite, table.name = 'bed')
sqlite.build(bed.file, connect.params)
chr <- c('chr10', 'chr1')
start <- c('100188904', '100185955')
end <- c('100188904', '100185955')
dat <- data.table(chr = chr, start = start, end = end)
x <- annotation.region.match(dat = dat, database.dir = tempdir(),
dbname_fixed = bed.sqlite, table_name_fixed = 'bed', 
db.type = 'sqlite', format_dat_fun = function(...) {
params = list(...);return(params[[1]])})
file.remove(bed.sqlite)