[Seqinr-commits] r1546 - pkg/man

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

Author: lobry
Date: 2009-02-04 14:56:30 +0100 (Wed, 04 Feb 2009)
New Revision: 1546

Added:
   pkg/man/peakabif.Rd
Log:
Function to locate peaks in ABIF data

Added: pkg/man/peakabif.Rd
===================================================================
--- pkg/man/peakabif.Rd	                        (rev 0)
+++ pkg/man/peakabif.Rd	2009-02-04 13:56:30 UTC (rev 1546)
@@ -0,0 +1,61 @@
+\name{peakabif}
+\alias{peakabif}
+\title{Peak location extraction for ABIF data}
+\description{
+  Simple peak location for data imported with the \code{\link{read.abif}} function
+  using cubic spline interpolation.
+}
+\usage{
+peakabif(abifdata, 
+  chanel, 
+  npeak, 
+  thres = 400/yscale, 
+  fig = TRUE,
+  chanel.names = c(1:4,105),
+  DATA = paste("DATA", chanel.names[chanel], sep = "."),
+  tmin = 1/tscale,
+  tmax = abifdata$Data[["SCAN.1"]]/tscale,
+  tscale = 1000, 
+  yscale = 1000,
+  irange = (tmin*tscale):(tmax*tscale),
+  y = abifdata$Data[[DATA]][irange]/yscale,
+  method = "monoH.FC",
+  ...)
+}
+\arguments{
+  \item{abifdata}{the result returned by \code{\link{read.abif}}}
+  \item{chanel}{the dye number}
+  \item{npeak}{the expected number of peaks}
+  \item{thres}{scaled threshold value}
+  \item{fig}{logical: should localized peaks be plotted}
+  \item{chanel.names}{numbers extensions used for the DATA}
+  \item{DATA}{names of the DATA components}
+  \item{tmin}{scaled starting time for the time axis}
+  \item{tmax}{scaled ending time for the time axis}
+  \item{tscale}{scale factor for the time axis}
+  \item{yscale}{scale factor for the y-axis (RFU)}
+  \item{irange}{indices of data to be plotted}
+  \item{y}{values used for the y-axis}
+  \item{method}{method to be used by \code{\link{splinefun}}}
+  \item{...}{arguments forwarded to \code{\link{plot}}}
+}
+\value{
+  Returns invisibly the unscaled values for the location of peaks.
+}
+\references{
+  \code{citation("seqinr")}
+}
+\author{J.R. Lobry}
+\seealso{
+  function \code{\link{read.abif}} to import files in ABIF format, 
+  \code{\link{plotabif}} to plot them,
+  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,
+  data \code{\link{ECH}} for an example of an allelic lader.
+}
+\examples{
+data(JLO)
+JLO.maxis <- peakabif(JLO, 5, npeak = 14, tmin = 2.7, thres = 0.1)
+}
+