1. gmapR
  2. man
  3. TP53Genome.Rd
Browse code

TP53 genome is now named by the TxDb package from which the TP53 region was retrieved, so that it is automatically refreshed with annotation changes, and devel and release can coexist.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@87282 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 10/03/2014 23:10:51
Showing 1 changed files
man/TP53Genome.Rd
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@@ -19,7 +19,9 @@ TP53Which()
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   For \code{TP53Genome}, a \code{GmapGenome} object. If this is the
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   first time the user has run this function, a side-effect will be the
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   generation of an on-disk genome index, under the name
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-  \dQuote{TP53_demo} in the default genome directory.
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+  \dQuote{TP53_demo_VERSION} in the default genome directory, where
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+  \code{VERSION} is the version of the TxDb package providing the bounds
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+  of the P53 gene.
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   For \code{TP53Which}, a \code{GRanges} of the extents of the TP53
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   gene, translated to the space of \code{TP53Genome}.
Browse code

Refactor various TP53Genome-related convenience functions. Makes it easier to get out genomic annotations in the TP53 genome space.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@69354 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 12/09/2012 05:14:34
Showing 1 changed files
man/TP53Genome.Rd
History View file @ abf2259
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@@ -1,5 +1,6 @@
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 \name{TP53Genome}
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 \alias{TP53Genome}
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+\alias{TP53Which}
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 \title{
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   Demo genome around TP53
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 }
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@@ -12,12 +13,16 @@
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 }
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 \usage{
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 TP53Genome()
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+TP53Which()
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 }
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 \value{
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-  A \code{GmapGenome} object. If this is the first time the user has run
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-  this function, a side-effect will be the generation of an on-disk
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-  genome index, under the name \dQuote{TP53_demo} in the default genome
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-  directory.
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+  For \code{TP53Genome}, a \code{GmapGenome} object. If this is the
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+  first time the user has run this function, a side-effect will be the
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+  generation of an on-disk genome index, under the name
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+  \dQuote{TP53_demo} in the default genome directory.
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+
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+  For \code{TP53Which}, a \code{GRanges} of the extents of the TP53
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+  gene, translated to the space of \code{TP53Genome}.
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 }
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 \author{
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   Michael Lawrence, Cory Barr
Browse code

Add TP53Genome function

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@69157 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 06/09/2012 23:14:14
Showing 1 changed files
man/TP53Genome.Rd
History View file @ 2256145
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new file mode 100644
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@@ -0,0 +1,28 @@
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+\name{TP53Genome}
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+\alias{TP53Genome}
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+\title{
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+  Demo genome around TP53
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+}
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+\description{
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+  Returns a \code{\linkS4class{GmapGenome}} object consisting of the
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+  UCSC hg19 sequence centered on the region of the TP53 gene, with 1 Mb
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+  flanking sequence on each side. This is intended as a
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+  test/demonstration genome and can be used, e.g., in conjunction with
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+  the \code{LungCancerLines} data package.
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+}
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+\usage{
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+TP53Genome()
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+}
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+\value{
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+  A \code{GmapGenome} object. If this is the first time the user has run
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+  this function, a side-effect will be the generation of an on-disk
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+  genome index, under the name \dQuote{TP53_demo} in the default genome
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+  directory.
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+}
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+\author{
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+  Michael Lawrence, Cory Barr
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+}
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+
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+\examples{
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+TP53Genome()
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+}