## File: stutterabif.Rd

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r-cran-seqinr 3.4-5-2
 1234567891011121314151617181920212223242526272829303132333435363738394041424344454647484950515253545556575859606162636465666768697071727374757677787980818283 \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") }