[med-svn] [r-bioc-annotationdbi] 01/04: New upstream version 1.40.0
Andreas Tille
tille at debian.org
Wed Nov 8 09:50:18 UTC 2017
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tille pushed a commit to branch master
in repository r-bioc-annotationdbi.
commit 371fca379cdca02297d39086d87747aa2dfd6f3a
Author: Andreas Tille <tille at debian.org>
Date: Wed Nov 8 10:45:04 2017 +0100
New upstream version 1.40.0
---
DESCRIPTION | 6 ++---
NAMESPACE | 12 ++++++++--
R/AllGenerics.R | 2 +-
R/Bimap.R | 2 ++
R/BimapFormatting.R | 2 ++
R/SQL.R | 1 -
R/methods-geneCentricDbs.R | 3 +++
build/vignette.rds | Bin 385 -> 385 bytes
inst/doc/AnnotationDbi.R | 6 ++---
inst/doc/AnnotationDbi.pdf | Bin 167097 -> 195011 bytes
inst/doc/IntroToAnnotationPackages.R | 42 ++++++++++++++++-----------------
inst/doc/IntroToAnnotationPackages.pdf | Bin 138388 -> 168435 bytes
man/Bimap-toTable.Rd | 1 +
man/BimapFormatting.Rd | 1 +
man/orgPackageName.Rd | 34 ++++++++++++++++++++++++++
15 files changed, 81 insertions(+), 31 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 93c8467..4e1ff86 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,12 +2,12 @@ Package: AnnotationDbi
Title: Annotation Database Interface
Description: Provides user interface and database connection code
for annotation data packages using SQLite data storage.
-Version: 1.38.2
+Version: 1.40.0
Encoding: UTF-8
Author: Hervé Pagès, Marc Carlson, Seth Falcon, Nianhua Li
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
Depends: R (>= 2.7.0), methods, utils, stats4, BiocGenerics (>=
- 0.15.10), Biobase (>= 1.17.0), IRanges
+ 0.23.1), Biobase (>= 1.17.0), IRanges
Imports: methods, utils, DBI, RSQLite, stats4, BiocGenerics, Biobase,
S4Vectors (>= 0.9.25), IRanges
Suggests: DBI (>= 0.2-4), RSQLite (>= 0.6-4), hgu95av2.db, GO.db,
@@ -34,6 +34,6 @@ Collate: 00RTobjs.R unlist2.R utils.R SQL.R AllGenerics.R AllClasses.R
License: Artistic-2.0
biocViews: Annotation, Microarray, Sequencing, GenomeAnnotation
VignetteBuilder: knitr
-Packaged: 2017-07-26 22:27:32 UTC; biocbuild
+Packaged: 2017-10-30 22:45:41 UTC; biocbuild
Video: https://www.youtube.com/watch?v=8qvGNTVz3Ik
NeedsCompilation: no
diff --git a/NAMESPACE b/NAMESPACE
index 60452df..ba10c29 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -129,7 +129,8 @@ exportMethods(
"columns",
"keytypes",
"select",
- "mapIds"
+ "mapIds",
+ "orgPackageName"
)
export(
@@ -180,5 +181,12 @@ export(
## AnnotationDb
metadata,
- createSimpleBimap
+ createSimpleBimap,
+
+ ## S3 methods
+ as.list.Bimap,
+ as.data.frame.Bimap
)
+
+S3method(as.list, Bimap)
+S3method(as.data.frame, Bimap)
diff --git a/R/AllGenerics.R b/R/AllGenerics.R
index 88fc983..cbe9a2e 100644
--- a/R/AllGenerics.R
+++ b/R/AllGenerics.R
@@ -46,7 +46,6 @@ setGeneric("getKEGGFrameData", function(x) standardGeneric("getKEGGFrameData"))
setGeneric("GOID", function(object) standardGeneric("GOID"))
setGeneric("Term", function(object) standardGeneric("Term"))
-setGeneric("Ontology", function(object) standardGeneric("Ontology"))
setGeneric("Definition", function(object) standardGeneric("Definition"))
setGeneric("Synonym", function(object) standardGeneric("Synonym"))
setGeneric("Secondary", function(object) standardGeneric("Secondary"))
@@ -62,6 +61,7 @@ setGeneric("Rtablename", function(x) standardGeneric("Rtablename"))
setGeneric("Lfilter", function(x) standardGeneric("Lfilter"))
setGeneric("Rfilter", function(x) standardGeneric("Rfilter"))
setGeneric("flatten", function(x, ...) standardGeneric("flatten"))
+setGeneric("orgPackageName", function(x, ...) standardGeneric("orgPackageName"))
## AnnotationDb
setGeneric("saveDb", signature="x",
diff --git a/R/Bimap.R b/R/Bimap.R
index dcd1cd4..6a95525 100644
--- a/R/Bimap.R
+++ b/R/Bimap.R
@@ -1103,6 +1103,8 @@ setMethod("toTable", "Bimap",
}
)
+as.data.frame.Bimap <- function(x, row.names = NULL, optional = FALSE, ...)
+ as.data.frame(x, row.names=row.names, optional=optional, ...)
setMethod("as.data.frame", "Bimap", toTable)
diff --git a/R/BimapFormatting.R b/R/BimapFormatting.R
index 1efca59..3b6a1fd 100644
--- a/R/BimapFormatting.R
+++ b/R/BimapFormatting.R
@@ -241,6 +241,8 @@
### The "as.list" methods.
###
+as.list.Bimap <- function(x, ...) as.list(x)
+
setMethod("as.list", "FlatBimap",
function(x, ...)
{
diff --git a/R/SQL.R b/R/SQL.R
index 1b79959..cf68972 100644
--- a/R/SQL.R
+++ b/R/SQL.R
@@ -408,7 +408,6 @@ dbAttach <- function(conn, SQL){
dbClearResult(obj)
}
-
dbGetTable <- function(conn, tablename, extra.SQL=NULL)
{
SQL <- paste0("SELECT * FROM ", tablename)
diff --git a/R/methods-geneCentricDbs.R b/R/methods-geneCentricDbs.R
index fab0c4b..53a864b 100644
--- a/R/methods-geneCentricDbs.R
+++ b/R/methods-geneCentricDbs.R
@@ -917,6 +917,9 @@ testForValidKeytype <- function(x, keytype){
if (!is.character(keys)){
stop("'keys' must be a character vector")
}
+ if (length(keys) == 0L) {
+ return()
+ }
if(is.null(fks)){ ## Normally, fks is just NULL and so we will call keys()
ktKeys <- keys(x, keytype)
}else{ ## This lets the caller say wait: use these keys instead
diff --git a/build/vignette.rds b/build/vignette.rds
index 81bb61f..c0ac96c 100644
Binary files a/build/vignette.rds and b/build/vignette.rds differ
diff --git a/inst/doc/AnnotationDbi.R b/inst/doc/AnnotationDbi.R
index cd79dde..2c1dd76 100644
--- a/inst/doc/AnnotationDbi.R
+++ b/inst/doc/AnnotationDbi.R
@@ -1,11 +1,11 @@
-## ----style, eval=TRUE, echo=FALSE, results='asis'---------------------------------------
+## ----style, eval=TRUE, echo=FALSE, results='asis'--------------------------
BiocStyle::latex()
-## ----include=FALSE----------------------------------------------------------------------
+## ----include=FALSE---------------------------------------------------------
library(knitr)
opts_chunk$set(tidy=FALSE)
-## ----<available schemas, results='hide'-------------------------------------------------
+## ----<available schemas, results='hide'------------------------------------
library(DBI)
library(org.Hs.eg.db)
library(AnnotationForge)
diff --git a/inst/doc/AnnotationDbi.pdf b/inst/doc/AnnotationDbi.pdf
index 8c3dd0a..d5b8928 100644
Binary files a/inst/doc/AnnotationDbi.pdf and b/inst/doc/AnnotationDbi.pdf differ
diff --git a/inst/doc/IntroToAnnotationPackages.R b/inst/doc/IntroToAnnotationPackages.R
index fc39739..bfe9149 100644
--- a/inst/doc/IntroToAnnotationPackages.R
+++ b/inst/doc/IntroToAnnotationPackages.R
@@ -1,72 +1,72 @@
-## ----style, eval=TRUE, echo=FALSE, results='asis'---------------------------------------
+## ----style, eval=TRUE, echo=FALSE, results='asis'--------------------------
BiocStyle::latex()
-## ----include=FALSE----------------------------------------------------------------------
+## ----include=FALSE---------------------------------------------------------
library(knitr)
opts_chunk$set(tidy=FALSE)
-## ----loadChip---------------------------------------------------------------------------
+## ----loadChip--------------------------------------------------------------
library(hgu95av2.db)
-## ----listContents-----------------------------------------------------------------------
+## ----listContents----------------------------------------------------------
ls("package:hgu95av2.db")
-## ----show-------------------------------------------------------------------------------
+## ----show------------------------------------------------------------------
hgu95av2.db
-## ----columns----------------------------------------------------------------------------
+## ----columns---------------------------------------------------------------
columns(hgu95av2.db)
-## ----help, eval=FALSE-------------------------------------------------------------------
+## ----help, eval=FALSE------------------------------------------------------
# help("SYMBOL")
-## ----keytypes---------------------------------------------------------------------------
+## ----keytypes--------------------------------------------------------------
keytypes(hgu95av2.db)
-## ----keys-------------------------------------------------------------------------------
+## ----keys------------------------------------------------------------------
head(keys(hgu95av2.db, keytype="SYMBOL"))
-## ----selectChip-------------------------------------------------------------------------
+## ----selectChip------------------------------------------------------------
#1st get some example keys
k <- head(keys(hgu95av2.db,keytype="PROBEID"))
# then call select
select(hgu95av2.db, keys=k, columns=c("SYMBOL","GENENAME"), keytype="PROBEID")
-## ----mapIdsChip-------------------------------------------------------------------------
+## ----mapIdsChip------------------------------------------------------------
#1st get some example keys
k <- head(keys(hgu95av2.db,keytype="PROBEID"))
# then call mapIds
mapIds(hgu95av2.db, keys=k, column=c("GENENAME"), keytype="PROBEID")
-## ----selectOrg1-------------------------------------------------------------------------
+## ----selectOrg1------------------------------------------------------------
library(org.Hs.eg.db)
columns(org.Hs.eg.db)
-## ----selectOrg2, eval=FALSE-------------------------------------------------------------
+## ----selectOrg2, eval=FALSE------------------------------------------------
# help("SYMBOL") ## for explanation of these columns and keytypes values
-## ----selectOrg3-------------------------------------------------------------------------
+## ----selectOrg3------------------------------------------------------------
keytypes(org.Hs.eg.db)
uniKeys <- head(keys(org.Hs.eg.db, keytype="UNIPROT"))
cols <- c("SYMBOL", "PATH")
select(org.Hs.eg.db, keys=uniKeys, columns=cols, keytype="UNIPROT")
-## ----selectData-------------------------------------------------------------------------
+## ----selectData------------------------------------------------------------
load(system.file("extdata", "resultTable.Rda", package="AnnotationDbi"))
head(resultTable)
-## ----selectOrgData----------------------------------------------------------------------
+## ----selectOrgData---------------------------------------------------------
annots <- select(org.Hs.eg.db, keys=rownames(resultTable),
columns=c("SYMBOL","GENENAME"), keytype="ENTREZID")
resultTable <- merge(resultTable, annots, by.x=0, by.y="ENTREZID")
head(resultTable)
-## ----selectGO---------------------------------------------------------------------------
+## ----selectGO--------------------------------------------------------------
library(GO.db)
GOIDs <- c("GO:0042254","GO:0044183")
select(GO.db, keys=GOIDs, columns="DEFINITION", keytype="GOID")
-## ----selectTxDb-------------------------------------------------------------------------
+## ----selectTxDb------------------------------------------------------------
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
txdb
@@ -77,7 +77,7 @@ cols <- c("TXID", "TXSTART")
select(txdb, keys=keys, columns=cols, keytype="GENEID")
-## ----selectEnsDb------------------------------------------------------------------------
+## ----selectEnsDb-----------------------------------------------------------
library(EnsDb.Hsapiens.v75)
edb <- EnsDb.Hsapiens.v75
edb
@@ -95,7 +95,7 @@ keys <- head(keys(edb, keytype="GENEID"))
select(edb, keys=keys, columns=c("TXID", "TXSEQSTART", "TXBIOTYPE"),
keytype="GENEID")
-## ----selectEnsDb.Y----------------------------------------------------------------------
+## ----selectEnsDb.Y---------------------------------------------------------
## Retrieve all gene IDs of all lincRNAs encoded on chromosome Y
linkY <- keys(edb,
filter=list(GenebiotypeFilter("lincRNA"), SeqnameFilter("Y")))
@@ -111,6 +111,6 @@ txs <- select(edb, keys=list(GenebiotypeFilter("lincRNA"), SeqnameFilter("Y")),
columns=c("TXID", "TXSEQSTART", "TXBIOTYPE"))
nrow(txs)
-## ----SessionInfo, echo=FALSE------------------------------------------------------------
+## ----SessionInfo, echo=FALSE-----------------------------------------------
sessionInfo()
diff --git a/inst/doc/IntroToAnnotationPackages.pdf b/inst/doc/IntroToAnnotationPackages.pdf
index 35486a9..9e4d0a2 100644
Binary files a/inst/doc/IntroToAnnotationPackages.pdf and b/inst/doc/IntroToAnnotationPackages.pdf differ
diff --git a/man/Bimap-toTable.Rd b/man/Bimap-toTable.Rd
index de8e99a..b658fb0 100644
--- a/man/Bimap-toTable.Rd
+++ b/man/Bimap-toTable.Rd
@@ -6,6 +6,7 @@
\alias{toTable,FlatBimap-method}
\alias{toTable,Bimap-method}
\alias{as.data.frame,Bimap-method}
+\alias{as.data.frame.Bimap}
\alias{nrow}
\alias{nrow,Bimap-method}
diff --git a/man/BimapFormatting.Rd b/man/BimapFormatting.Rd
index d604cd6..cb6ee16 100644
--- a/man/BimapFormatting.Rd
+++ b/man/BimapFormatting.Rd
@@ -5,6 +5,7 @@
\alias{as.list}
\alias{as.list,FlatBimap-method}
\alias{as.list,Bimap-method}
+\alias{as.list.Bimap}
\alias{as.list,IpiAnnDbMap-method}
\alias{as.list,AgiAnnDbMap-method}
\alias{as.list,GoAnnDbBimap-method}
diff --git a/man/orgPackageName.Rd b/man/orgPackageName.Rd
new file mode 100644
index 0000000..f6619ab
--- /dev/null
+++ b/man/orgPackageName.Rd
@@ -0,0 +1,34 @@
+\name{orgPackageName}
+
+\alias{orgPackageName}
+
+\title{Org package contained in annotation object}
+
+\description{
+ Get the name of the org package used by an annotation resource object.
+
+ NOTE: This man page is for the \code{orgPackageName} \emph{S4 generic
+ function} defined in the \pkg{AnnotationDbi} package.
+ Bioconductor packages can define specific methods for annotation
+ objects not supported by the default method.
+}
+
+\usage{
+orgPackageName(x, ...)
+}
+
+\arguments{
+ \item{x}{
+ An annotation resource object.
+ }
+ \item{...}{
+ Additional arguments.
+ }
+}
+
+\value{
+ A \code{character(1)} vector indicating the org package name.
+
+ Specific methods defined in Bioconductor packages should
+ behave as consistently as possible with the default method.
+}
--
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