update DESCRIPTION and document

DESCRIPTION

@@ -1,10 +1,10 @@
 Package: annovarR
 Type: Package
-Title: Integrated Tool to Annotate Genetic Variants
+Title: Integrated Framework to Annotate Genetic Variants
 Version: 1.0.0
 Authors@R: person("Jianfeng", "Li", email = "[email protected]", role = c("aut", "cre"))
 Description: 
-    Can be used to annotate genetic variants from genomic and transcriptome data. Published and in-house databases were introduced in 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.
 Depends:
     R (>= 3.3.0)
 URL: https://github.com/JhuangLab/annovarR

R/annotation.R

@@ -115,10 +115,12 @@ annotation.cols.match <- function(dat = data.table(), anno.name = "", buildver =
 #' 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]])})
+#' \dontrun{
+#' 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)
 annotation.region.match <- function(dat = data.table(), anno.name = "", buildver = "hg19", 
   database.dir = Sys.getenv("annovarR_DB_DIR", ""), db.col.order = 1:3, index.cols = c("chr", 

R/annovarR.R

@@ -1,6 +1,13 @@
-#' annovarR is an integrated database and tool to annotate genetic variants 
-#' from genomic and transcriptome sequencing data.
-#' This work mainly based on ANNOVAR and other public annotation databases.
+#' 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' (\url{http://asia.ensembl.org/info/docs/tools/vep/index.html}), 
+#' 'ANNOVAR' (\url{http://annovar.openbioinformatics.org/}), 'vcfanno' (\url{https://github.com/brentp/vcfanno})
+#' and 'AnnotationDbi' (\url{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.
 #' 
 #' @author
 #' Li Jianfeng \url{[email protected]}

R/auto.R

@@ -185,9 +185,11 @@ sqlite.auto.index <- function(anno.name = "", buildver = "hg19", database.dir =
 #' i <- 'hg19_avsnp147'
 #' database <- system.file('extdata', sprintf('demo/%s.txt', i), package = 'annovarR')
 #' file.copy(database, sprintf('%s/%s.txt', tempdir(), i))
-#' ## mysql.auto.build(anno.name = 'avsnp147', database.dir = tempdir(), 
-#' ## mysql.connect.params = list(user = 'username', password = 'password', 
-#' ## host = 'localhost', port = 3306, dbname = 'annovarR'))
+#' \dontrun{
+#'  mysql.auto.build(anno.name = 'avsnp147', database.dir = tempdir(), 
+#'  mysql.connect.params = list(user = 'username', password = 'password', 
+#'  host = 'localhost', port = 3306, dbname = 'annovarR'))
+#' }
 mysql.auto.build <- function(anno.name = "", buildver = "hg19", database.dir = "/path/", 
   mysql.connect.params = list(user = "", password = "", host = "localhost", port = "3306"), 
   overwrite = FALSE, append = FALSE, index = "chr_start_index", db.type = "mysql", 
@@ -282,9 +284,11 @@ mysql.auto.build <- function(anno.name = "", buildver = "hg19", database.dir = "
 #' i <- 'hg19_avsnp147'
 #' database <- system.file('extdata', sprintf('demo/%s.txt', i), package = 'annovarR')
 #' file.copy(database, sprintf('%s/%s.txt', tempdir(), i))
-#' ## mysql.auto.index(anno.name = 'avsnp147', database.dir = tempdir(), 
-#' ## mysql.connect.params = list(user = 'username', password = 'password', 
-#' ## host = 'localhost', port = 3306, dbname = 'annovarR'))
+#' \dontrun{
+#'  mysql.auto.index(anno.name = 'avsnp147', database.dir = tempdir(), 
+#'  mysql.connect.params = list(user = 'username', password = 'password', 
+#'  host = 'localhost', port = 3306, dbname = 'annovarR'))
+#' }
 mysql.auto.index <- function(anno.name = "", buildver = "hg19", database.dir = "/path/", 
   mysql.connect.params = list(user = "", password = "", host = "localhost", port = "3306"), 
   index = "chr_start_index", db.type = "mysql", database.cfg = system.file("extdata", 

R/build.R

@@ -169,8 +169,10 @@ drop.sqlite.index <- function(sqlite.connect.params = list(dbname = "", table.na
 #' @export
 #' @examples
 #' test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'annovarR')
-#' ##mysql.build(test.dat, list(host = 'host', dbname = 'db', 
-#' ##table.name = 'table', user = 'user', password = 'password'))
+#' \dontrun{
+#' mysql.build(test.dat, list(host = 'host', dbname = 'db', 
+#' table.name = 'table', user = 'user', password = 'password'))
+#' }
 mysql.build <- function(filename = "", mysql.connect.params = list(host = "", dbname = "", 
   table.name = "", user = "", password = ""), dat = data.table(), fread.params = list(), 
   new.colnames = NULL, verbose = FALSE, ...) {
@@ -219,8 +221,10 @@ mysql.build <- function(filename = "", mysql.connect.params = list(host = "", db
 #' @export
 #' @examples
 #' test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'annovarR')
-#' ##mysql.index(list(host = 'host', dbname = 'db', table.name = 'table', 
-#' ##user = 'user', password = 'password'), index = 'index_name', cols = c('V1', 'V2'))
+#' \dontrun{
+#' mysql.index(list(host = 'host', dbname = 'db', table.name = 'table', 
+#' user = 'user', password = 'password'), index = 'index_name', cols = c('V1', 'V2'))
+#' }
 mysql.index <- function(mysql.connect.params = list(host = "", dbname = "", table.name = "", 
   user = "user", password = "password"), index = "", cols = c(), verbose = FALSE, 
   ...) {
@@ -262,8 +266,10 @@ mysql.index <- function(mysql.connect.params = list(host = "", dbname = "", tabl
 #' @export
 #' @examples
 #' test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'annovarR')
-#' ##drop.mysql.index(list(host = 'host', dbname = 'db', user = 'user', password = 'password'), 
-#' ##index = 'index_name')
+#' \dontrun{
+#' drop.mysql.index(list(host = 'host', dbname = 'db', user = 'user', password = 'password'), 
+#' index = 'index_name')
+#' }
 drop.mysql.index <- function(mysql.connect.params = list(host = "", dbname = "", 
   table.name = "", user = "user", password = "password"), index = "", verbose = FALSE, 
   ...) {

R/get.R

@@ -124,8 +124,10 @@ sqlite.tb.colnames <- function(sqlite.connect.params = list(dbname = "", table.n
 #' @param ... Other parameters pass to dbConnect
 #' @export
 #' @examples
-#' ##mysql.db.colnames(list(host = 'host', dbname = 'db', user = 'user', 
-#' ##password = 'password', table.name = 'table'))
+#' \dontrun{
+#' mysql.db.colnames(list(host = 'host', dbname = 'db', user = 'user', 
+#' password = 'password', table.name = 'table'))
+#' }
 mysql.tb.colnames <- function(mysql.connect.params = list(host = "", dbname = "", 
   user = "", password = "", table.name = ""), ...) {
   mysql.connect.params <- config.list.merge(list(MySQL()), mysql.connect.params)