rename annovarR to anor

.vscode/tasks.json

@@ -0,0 +1,24 @@
+{
+  // See https://go.microsoft.com/fwlink/?LinkId=733558
+  // for the documentation about the tasks.json format
+  "version": "2.0.0",
+  "tasks": [
+    {
+      "label": "build",
+      "type": "shell",
+      "command": "make build"
+    },
+    {
+      "label": "test",
+      "type": "shell",
+      "command": "make test",
+      "problemMatcher": []
+    },
+    {
+      "label": "pkgdown_build",
+      "type": "shell",
+      "command": "Rscript -e 'pkgdown::build_site()'",
+      "problemMatcher": []
+    },
+  ]
+}

ChangeLog

@@ -74,7 +74,7 @@
 
 2018-02-26 Li Jianfeng <[email protected]>
 
-		* initial annovarR shiny App (inst/extdata/tools/shiny)
+		* initial anor shiny App (inst/extdata/tools/shiny)
 
 2018-01-19 Li Jianfeng <[email protected]>
 

DESCRIPTION

@@ -1,14 +1,14 @@
-Package: annovarR
+Package: anor
 Type: Package
 Title: Integrated Framework to Annotate Genetic Variants
 Version: 1.3
 Authors@R: person("Jianfeng", "Li", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2349-208X"))
 Description: 
-    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.
+    The 'anor' 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 'anor' 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 'anor'. For example, 'anor' 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
-BugReports: https://github.com/JhuangLab/annovarR/issues
+URL: https://github.com/JhuangLab/anor
+BugReports: https://github.com/JhuangLab/anor/issues
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
@@ -29,7 +29,7 @@ Imports:
     devtools,
     AnnotationDbi,
     liteq
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.0
 Suggests: testthat,
     knitr,
     rmarkdown,

Dockerfile

@@ -3,10 +3,10 @@ FROM bioinstaller/ngsjs:latest
 ## This handle reaches Jianfeng
 MAINTAINER "Jianfeng Li" [email protected]
 
-ADD . /tmp/annovarR
+ADD . /tmp/anor
 
 Run runuser -s /bin/bash -l opencpu -c "Rscript -e 'pacman::p_load(maftools, clusterProfiler, CEMiTool, org.Hs.eg.db, DT)'" \
-    && runuser -s /bin/bash -l opencpu -c "Rscript -e 'devtools::install(\"/tmp/annovarR\", dependences = T)'" \
-    && rm -rf /tmp/annovarR \
+    && runuser -s /bin/bash -l opencpu -c "Rscript -e 'devtools::install(\"/tmp/anor\", dependences = T)'" \
+    && rm -rf /tmp/anor \
     && rm -rf /var/lib/apt/lists/* \
     && rm -rf /tmp/downloaded_packages/ /tmp/*.rds

Makefile

@@ -2,7 +2,7 @@ PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
 PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
 PKGSRC  := $(shell basename `pwd`)
 
-all: doc build check_cran
+all: doc build check
 
 doc:
 	Rscript -e "devtools::document()"

NEWS.md

@@ -1,10 +1,10 @@
-# annovarR 1.1.0
+# anor 1.1.0
 
 ## New features
 
 * Shiny app for maftools and gvmap
 
-# annovarR 1.0.0
+# anor 1.0.0
 
 ## New features
 

R/annotation.R

@@ -33,13 +33,13 @@
 #' end <- c('10020', '10020', '10020')
 #' ref <- c('A', 'A', 'A')
 #' alt <- c('-', '-', '-')
-#' database <- system.file('extdata', 'demo/hg19_avsnp147.txt', package = 'annovarR')
+#' 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.cols.match(dat, 'avsnp147', database.dir = database.dir, 
 #' return_col_names = 'avSNP147', db.type = 'txt')
 annotation.cols.match <- function(dat = data.table(), anno.name = "", buildver = "hg19", 
-  database.dir = Sys.getenv("annovarR_DB_DIR", ""), db_col_order = 1:5, index_cols = c("chr", 
+  database.dir = Sys.getenv("anor_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, 
@@ -108,7 +108,7 @@ annotation.cols.match <- function(dat = data.table(), anno.name = "", buildver =
 #' @export
 #' @examples
 #' library(data.table)
-#' bed.file <- system.file('extdata', 'demo/example.bed', package = 'annovarR')
+#' 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)
@@ -122,7 +122,7 @@ annotation.cols.match <- function(dat = data.table(), anno.name = "", buildver =
 #' 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", 
+  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, 
@@ -184,7 +184,7 @@ annotation.region.match <- function(dat = data.table(), anno.name = "", buildver
 #' the names can be found on the http://annovar.openbioinformatics.org/en/latest/user-guide/download/
 #' @param database.dir Dir of the databases
 #' @param db.type Setting the database type (sqlite or txt)
-#' @param database.cfg Configuration file of annovarR databases infomation
+#' @param database.cfg Configuration file of anor databases infomation
 #' @param func Function to anntate the dat data, default is to search the function in extdata/database.toml
 #' @param mysql.connect.params Connect MySQL database other parameters, 
 #' e.g. list(host='11.11.11.1', port = '3306', user = '', password = '123456')
@@ -199,14 +199,14 @@ annotation.region.match <- function(dat = data.table(), anno.name = "", buildver
 #' end <- c('10020', '10020', '10020')
 #' ref <- c('A', 'A', 'A')
 #' alt <- c('-', '-', '-')
-#' database <- system.file('extdata', 'demo/hg19_avsnp147.txt', package = 'annovarR')
+#' 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')
 annotation <- function(dat = data.table(), anno.name = "", buildver = "hg19", annovar.anno.names = "", 
-  database.dir = Sys.getenv("annovarR_DB_DIR", ""), db.type = NULL, database.cfg = system.file("extdata", 
-    "config/databases.toml", package = "annovarR"), func = NULL, mysql.connect.params = list(host = "", 
+  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 = ""), 
   ...) {
   if (length(anno.name) > 1) {
@@ -244,7 +244,7 @@ annotation <- function(dat = data.table(), anno.name = "", buildver = "hg19", an
 #' end <- c('10020', '10020', '10020')
 #' ref <- c('A', 'A', 'A')
 #' alt <- c('-', '-', '-')
-#' database <- system.file('extdata', 'demo/hg19_avsnp147.txt', package = 'annovarR')
+#' 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.merge(dat = dat, anno.names = c('avsnp147'), 
@@ -262,7 +262,7 @@ annotation.merge <- function(anno.names, ...) {
     })
     names(result.list.2) <- perl_annovar_names
     if (length(result.list.1) != 0) {
-      return(list(annovarR = as.data.table(result.list.1), annovar = result.list.2))
+      return(list(anor = as.data.table(result.list.1), annovar = result.list.2))
     } else {
       return(list(annovar = result.list.2))
     }

R/annotation.utils.R

@@ -1,6 +1,6 @@
 # preprocess before to query with database
 before.query.steps <- function(dat = data.table(), anno.name = "", buildver = "hg19", 
-  database.dir = Sys.getenv("annovarR_DB_DIR", ""), db_col_order = 1:5, index_cols = c("chr", 
+  database.dir = Sys.getenv("anor_DB_DIR", ""), db_col_order = 1:5, index_cols = c("chr", 
     "start"), matched_cols = c("chr", "start", "end", "ref", "alt"), format_dat_fun = format.cols, 
   dbname_fixed = NULL, table_name_fixed = NULL, setdb_fun = set.db, set_table_fun = set.table, 
   db.type = NULL, db.file.prefix = NULL, mysql.connect.params = list(), sqlite.connect.params = list(), 

R/annovarR.R → R/anor.R

@@ -1,25 +1,25 @@
-#' The 'annovarR' package provides R functions as well as database resources which offer an
+#' The 'anor' 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,
+#' The wrapper functions of 'anor' 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,
+#' Besides, massive published genetic variants annotation databases were integrated into 'anor'.
+#' For example, 'anor' 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]}
 #' @seealso
 #' Useful links:
 #'
-#' \url{https://github.com/JhuangLab/annovarR}
+#' \url{https://github.com/JhuangLab/anor}
 #'
-#' Report bugs at \url{https://github.com/JhuangLab/annovarR/issues}
+#' Report bugs at \url{https://github.com/JhuangLab/anor/issues}
 #'
 #' @docType package
-#' @name annovarR
+#' @name anor
 #' @import stringr DBI data.table futile.logger configr BioInstaller glue liteq
 #' @importFrom stringi stri_rand_strings
 #' @importFrom utils packageVersion head installed.packages compareVersion install.packages
@@ -35,9 +35,9 @@ 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)
+  # msg <- sprintf('anor %s \n', packageVersion('anor')) msg <-
+  # sprintf('%s Documentation: ?anor, example(anor) and
+  # browseVignettes(\'anor\')', msg) packageStartupMessage(msg)
   Sys.setenv(R_TESTS = "")
   invisible()
 }