File: peakabif.Rd

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\name{peakabif}
\alias{peakabif}
\title{Extraction of Peak locations, Heights and Surfaces from 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",
  maxrfu = 1000,
  ...)
}
\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{maxrfu}{argument passed to \code{\link{baselineabif}}}
  \item{...}{arguments forwarded to \code{\link{plot}}}
}
\value{
  Returns invisibly a list with the unscaled values for the locations of peaks,
  heights of peaks and surfaces of peaks and baseline estimate. The peak
  location are in datapoint units, that is an integer starting at 1 for the
  first experimental point, 2 for the second experimental point, etc. 
  However, due to interpolation between points
  the estimated peak location is usually not an integer.
}
\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)$maxis
}