R/annovarR.R

In annovarR: Integrated Framework to Annotate Genetic Variants

#' 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{lee_jianfeng@sjtu.edu.cn}
#' @seealso
#' Useful links:
#'
#' \url{https://github.com/JhuangLab/annovarR} 
#'
#' Report bugs at \url{https://github.com/JhuangLab/annovarR/issues} 
#'
#' @docType package
#' @name annovarR
#' @import stringr DBI data.table futile.logger configr BioInstaller glue
#' @importFrom stringi stri_rand_strings
#' @importFrom utils packageVersion head installed.packages
#' @importFrom RMySQL MySQL dbRemoveTable mysqlHasDefault
#' @importFrom RSQLite SQLite dbRemoveTable
#' @importFrom methods formalArgs
#' @importFrom ngstk split_list split_row_file batch_file
#' @importFrom AnnotationDbi select
#' @importFrom vcfR read.vcfR INFO2df getID getINFO getCHROM getPOS getFILTER getALT getFIX
NULL

.onAttach <- function(libname, pkgname) {
  op <- options()
  # msg <- sprintf('annovarR %s \n', packageVersion('annovarR')) msg <-
  # sprintf('%s Documentation: ?annovarR, example(annovarR) and
  # browseVignettes(\'annovarR\')', msg) packageStartupMessage(msg)
  Sys.setenv(R_TESTS = "")
  invisible()
}