[Seqinr-commits] r1665 - pkg/man

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

Author: lobry
Date: 2009-10-12 18:30:36 +0200 (Mon, 12 Oct 2009)
New Revision: 1665

Added:
   pkg/man/stutterabif.Rd
Log:
new function for stutter ratio

Added: pkg/man/stutterabif.Rd
===================================================================
--- pkg/man/stutterabif.Rd	                        (rev 0)
+++ pkg/man/stutterabif.Rd	2009-10-12 16:30:36 UTC (rev 1665)
@@ -0,0 +1,77 @@
+\name{stutterabif}
+\Rdversion{1.1}
+\alias{stutterabif}
+\title{Stutter ratio estimation}
+\description{
+This function tries to estimate the stutter ratio, either in terms of peak heigth ratios or peak
+surface ratio.
+}
+\usage{
+stutterabif(abifdata, chanel, poswild, datapointbefore = 70, datapointafter = 20, datapointsigma = 3.5, chanel.names = c(1:4, 105), DATA = paste("DATA", chanel.names[chanel], sep = "."), maxrfu = 1000, method = "monoH.FC", pms = 6, fig = FALSE)
+}
+\arguments{
+  \item{abifdata}{the result returned by \code{\link{read.abif}}}
+  \item{chanel}{the dye number}
+  \item{poswild}{the position in datapoint units of the allele at the origin of the stutter product, typically
+    obtained after a call to \code{\link{peakabif}}}
+  \item{datapointbefore}{how many datapoints before \code{poswild} to be include in analysis}
+  \item{datapointafter}{how many datapoints after \code{poswild} to be include in analysis}
+  \item{datapointsigma}{initial guess for the standard deviation of a peak}
+  \item{chanel.names}{numbers extensions used for the DATA}
+  \item{DATA}{names of the DATA components}
+  \item{maxrfu}{argument passed to \code{\link{baselineabif}}}
+  \item{method}{method to be used by \code{\link{splinefun}}}
+  \item{pms}{how many standard deviations (after gaussian fit) before and after the mean peak values should be
+     considered for spline function interpolation}
+  \item{fig}{should a summary plot be produced?}
+}
+
+\details{FIXME, See R code for now}
+
+\value{
+A list with the following components:
+\item{rh}{Stutter ratio computed as the height of the stutter divided by the height of its corresponding allele}
+\item{rs}{Stutter ratio computed as the surface of the stutter divided by the surface of its corresponding allele}
+\item{h1}{The height of the stutter with baseline at 0}
+\item{h2}{The height of the allele with baseline at 0}
+\item{s1}{The surface of the stutter}
+\item{s2}{The surface of the allele}
+\item{p}{A list of additional parameter that could be usesfull, see example}
+}
+
+\author{J.R. Lobry}
+
+\seealso{\code{\link{JLO}} for a dataset example, \code{\link{peakabif}} to get an estimate of peak location.}
+\examples{
+  #
+  # Load pre-defined dataset, same as what would be obtained with read.abif:
+  #
+
+data(JLO)
+
+  #
+  # Get peak locations in the blue channel:
+  #
+
+maxis <- peakabif(JLO, 1, npeak = 6, tmin = 3, fig = FALSE)$maxis
+
+  #
+  # Compute stutter ratio for first peak and ask for a figure:
+  #
+
+tmp <- stutterabif(JLO, 1, maxis[1], fig = TRUE)
+
+  #
+  # Show in addition the normal approximation used at the stutter peak:
+  #
+
+xx <- seq(tmp$p$mu1 - 6*tmp$p$sd1, tmp$p$mu1 + 6*tmp$p$sd1, le = 100)
+lines(xx, tmp$p$p1*dnorm(xx, tmp$p$mu1, tmp$p$sd1), col = "darkgreen")
+
+  #
+  # Show in addition the normal approximation used at allele peak:
+  #
+
+xx <- seq(tmp$p$mu2 - 6*tmp$p$sd2, tmp$p$mu2 + 6*tmp$p$sd2, le = 100)
+lines(xx, tmp$p$p2*dnorm(xx, tmp$p$mu2, tmp$p$sd2), col = "darkgreen")
+}