[Seqinr-commits] r1538 - pkg/man

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

Author: lobry
Date: 2009-01-23 18:53:14 +0100 (Fri, 23 Jan 2009)
New Revision: 1538

Added:
   pkg/man/ECH.Rd
   pkg/man/JLO.Rd
Log:
new STR raw data

Added: pkg/man/ECH.Rd
===================================================================
--- pkg/man/ECH.Rd	                        (rev 0)
+++ pkg/man/ECH.Rd	2009-01-23 17:53:14 UTC (rev 1538)
@@ -0,0 +1,37 @@
+\name{ECH}
+\alias{ECH}
+\docType{data}
+\title{Forensic Genetic Profile Allelic Ladder Raw Data}
+\description{
+  This is an example of allelic ladder raw data for a human STR genetic profile at 16 loci
+  (\emph{viz.} D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539,
+  D2S1338, D19S433, vWA, TPOX, D18S51, Amelogenin, D5S818, FGA) which
+  are commonly used in forensic sciences for individual identifications.
+}
+\usage{data(ECH)}
+\format{
+  A list with 3 components as in \code{\link{JLO}}
+}
+\source{
+  Data were kindly provided by the INPS (Institut National de Police Scientifique)
+  which is the national forensic sciences institute in France. Experiments
+  were done at the LPS (Laboratoire de Police Scientifique de Lyon) in 2008.
+}
+\references{
+  \code{citation("seqinr")}
+
+  Anonymous (2006) Applied Biosystem Genetic Analysis Data File Format.
+  Available at \url{http://www.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf}.
+  Last visited on 03-NOV-2008.
+}
+\author{J.R. Lobry}
+\seealso{
+  function \code{\link{read.abif}} to import files in ABIF format, 
+  data \code{\link{gs500liz}} for internal size standards,
+  data \code{\link{identifiler}} for allele names in the allelic ladder,
+  data \code{\link{JLO}} for an example of an individual sample file.
+}
+\examples{
+data(JLO)
+}
+

Added: pkg/man/JLO.Rd
===================================================================
--- pkg/man/JLO.Rd	                        (rev 0)
+++ pkg/man/JLO.Rd	2009-01-23 17:53:14 UTC (rev 1538)
@@ -0,0 +1,49 @@
+\name{JLO}
+\alias{JLO}
+\docType{data}
+\title{Forensic Genetic Profile Raw Data}
+\description{
+  This is an example of raw data for a human STR genetic profile at 16 loci
+  (\emph{viz.} D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539,
+  D2S1338, D19S433, vWA, TPOX, D18S51, Amelogenin, D5S818, FGA) which
+  are commonly used in forensic sciences for individual identifications.
+}
+\usage{data(JLO)}
+\format{
+  A list with 3 components.
+  \describe{
+    \item{Header}{a list corresponding to the header in the ABIF file}
+    \item{Directory}{a data.frame corresponding to the Directory in the ABIF file}
+    \item{Data}{a list with all raw data in the ABIF file.}
+  }
+}
+\details{
+  This dataset is the expected result when reading the file
+  \code{2_FAC321_0000205983_B02_004.fsa} with the
+  function \code{\link{read.abif}}. This dataset is used for
+  the quality check of this function.
+}
+\source{
+  The DNA source is from the author so that there are no privacy concern.
+  Data were kindly provided by the INPS (Institut National de Police Scientifique)
+  which is the national forensic sciences institute in France. Experiments
+  were done at the LPS (Laboratoire de Police Scientifique de Lyon) in 2008.
+}
+\references{
+  \code{citation("seqinr")}
+
+  Anonymous (2006) Applied Biosystem Genetic Analysis Data File Format.
+  Available at \url{http://www.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf}.
+  Last visited on 03-NOV-2008.
+}
+\author{J.R. Lobry}
+\seealso{
+  function \code{\link{read.abif}} to import files in ABIF format, 
+  data \code{\link{gs500liz}} for internal size standards,
+  data \code{\link{ECH}} for the corresponding allelic ladder,
+  data \code{\link{identifiler}} for allele names in the allelic ladder.
+}
+\examples{
+data(JLO)
+}
+