stutterabif: Stutter ratio estimation
In seqinr: Biological Sequences Retrieval and Analysis

stutterabif

R Documentation

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

`abifdata`	the result returned by `read.abif`
`chanel`	the dye number
`poswild`	the position in datapoint units of the allele at the origin of the stutter product, typically obtained after a call to `peakabif`
`datapointbefore`	how many datapoints before `poswild` to be include in analysis
`datapointafter`	how many datapoints after `poswild` to be include in analysis
`datapointsigma`	initial guess for the standard deviation of a peak
`chanel.names`	numbers extensions used for the DATA
`DATA`	names of the DATA components
`maxrfu`	argument passed to `baselineabif`
`method`	method to be used by `splinefun`
`pms`	how many standard deviations (after gaussian fit) before and after the mean peak values should be considered for spline function interpolation
`fig`	should a summary plot be produced?

Details

FIXME, See R code for now

Value

A list with the following components:

`rh`	Stutter ratio computed as the height of the stutter divided by the height of its corresponding allele
`rs`	Stutter ratio computed as the surface of the stutter divided by the surface of its corresponding allele
`h1`	The height of the stutter with baseline at 0
`h2`	The height of the allele with baseline at 0
`s1`	The surface of the stutter
`s2`	The surface of the allele
`p`	A list of additional parameter that could be usesfull, see example

Author(s)

J.R. Lobry

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")

seqinr documentation built on May 29, 2024, 6:36 a.m.