[Seqinr-commits] r1548 - pkg/man

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

Author: lobry
Date: 2009-02-04 14:58:36 +0100 (Wed, 04 Feb 2009)
New Revision: 1548

Added:
   pkg/man/plotladder.Rd
Log:
New function to plot allelic ladder in ABIF data

Added: pkg/man/plotladder.Rd
===================================================================
--- pkg/man/plotladder.Rd	                        (rev 0)
+++ pkg/man/plotladder.Rd	2009-02-04 13:58:36 UTC (rev 1548)
@@ -0,0 +1,59 @@
+\name{plotladder}
+\alias{plotladder}
+\title{Simple plot of an allelic ladder from ABIF data}
+\description{
+  Simple representation of an observed allelic ladder.
+}
+\usage{
+plotladder(abifdata, chanel, calibr, allele.names = "identifiler", npeak = NULL, ...)
+}
+\arguments{
+  \item{abifdata}{the result returned by \code{\link{read.abif}}}
+  \item{chanel}{the dye number}
+  \item{calibr}{a mandatory calibration function to convert time into bp}
+  \item{allele.names}{name of the dataset which contains allele names as in \code{link{identifiler}}}
+  \item{npeak}{expected number of peaks, deduced from \code{allele.names} by default}
+  \item{...}{arguments forwarded to \code{\link{peakabif}}}
+}
+\value{
+  Returns invisibly the location of peaks in bp.
+}
+\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{
+  #
+  # load an example of allelic ladder results from an ABIF (*.fsa) file:
+  #
+data(ECH)
+  #
+  # Extract from internal size standard chanel number 5 the location 
+  # of 14 peaks:
+  #
+ECH.maxis <- peakabif(ECH, 5, npeak = 14, tmin = 2.7, thres = 0.1, fig = FALSE)
+  #
+  # Load data about the expected size of peaks in bp for calibration:
+  #
+data(gs500liz)
+lizbp <- gs500liz$liz # All peaks size in bp
+lizbp[!gs500liz$mask1 | !gs500liz$mask2] <- NA # Mark useless peaks
+lizbp <- lizbp[-c(1,2)] # The first two peaks are not extracted from ECH
+ECH.calibr <- splinefun(ECH.maxis[!is.na(lizbp)], lizbp[!is.na(lizbp)])
+  #
+  # Show the allelic ladder for the 4 dyes:
+  #
+plotladder(ECH, 1, ECH.calibr, tmin = 3.1, thres = 0.3, fig = FALSE)
+plotladder(ECH, 2, ECH.calibr, tmin = 3.1, thres = 0.35, fig = FALSE)
+plotladder(ECH, 3, ECH.calibr, tmin = 3.1, thres = 0.2, fig = FALSE)
+plotladder(ECH, 4, ECH.calibr, tmin = 3.1, thres = 0.2, fig = FALSE)
+}
+