[Seqinr-commits] r2005 - pkg/man

[noreply at r-forge.r-project.org]

Author: jeanlobry
Date: 2016-10-09 13:26:32 +0200 (Sun, 09 Oct 2016)
New Revision: 2005

Added:
   pkg/man/gcT.Rd
Log:
 

Added: pkg/man/gcT.Rd
===================================================================
--- pkg/man/gcT.Rd	                        (rev 0)
+++ pkg/man/gcT.Rd	2016-10-09 11:26:32 UTC (rev 2005)
@@ -0,0 +1,34 @@
+\name{gcT}
+\alias{gcT}
+\docType{data}
+\title{GC content and temperature in bacteria}
+\description{
+  This data set was used in Galtier and Lobry (1997) to study the relationship between the optimal growth temperature of bacteria and their G+C content at the genomic level and locally were selection is active to maintain secondary structures in the stems of RNAs.
+}
+\format{
+ 	\code{gcT} is a list containing the 9 following components:  
+	\describe{	
+ 	\item{species}{is a data frame containing the optimal growth temperature and genomic G+C content for 772 bacterial species. Detailled explanations for this table and the following are available in the \code{README} component.}
+ 	\item{genus}{is a data frame containing the optimal growth temperature and genomic G+C content for 224 bacterial genus.}
+ 	\item{details}{is a data frame with more information, see \code{README}.}
+ 	\item{gc16S}{is a data frame containing the optimal growth temperature and stems G+C content for 16S RNA from 165 bacterial genus.}
+ 	\item{gctRNA}{is a data frame containing the optimal growth temperature and stems G+C content for tRNA from 51 bacterial genus.}
+ 	\item{gc23S}{is a data frame containing the optimal growth temperature and stems G+C content for 23S RNA from 38 bacterial genus.}
+ 	\item{gc5S}{is a data frame containing the optimal growth temperature and stems G+C content for 5S RNA from 71 bacterial genus.}
+ 	\item{README}{is the original README file from \code{ftp://biom3.univ-lyon1.fr/pub/datasets/JME97/} last updated 13-MAY-2002.}
+ 	\item{importgcT}{is the R script used to import data.}
+  }
+}
+\source{
+Galtier, N. & Lobry, J.R. (1997). Relationships between genomic G+C 
+content, RNA secondary structures, and optimal growth temperature 
+in prokaryotes. \emph{Journal of Molecular Evolution} \bold{44}:632-636.\cr
+
+Data imported into seqinr with the R script given in the last component of the dataset by J.R. Lobry on 09-OCT-2016. 
+}
+\references{
+  \code{citation("seqinr")}
+}
+\examples{
+data(gcT)
+}