peakabif: Extraction of Peak locations, Heights and Surfaces from ABIF...

In seqinr: Biological Sequences Retrieval and Analysis

Extraction of Peak locations, Heights and Surfaces from ABIF data

Description

Simple peak location for data imported with the 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

abifdata	the result returned by read.abif
chanel	the dye number
npeak	the expected number of peaks
thres	scaled threshold value
fig	logical: should localized peaks be plotted
chanel.names	numbers extensions used for the DATA
DATA	names of the DATA components
tmin	scaled starting time for the time axis
tmax	scaled ending time for the time axis
tscale	scale factor for the time axis
yscale	scale factor for the y-axis (RFU)
irange	indices of data to be plotted
y	values used for the y-axis
method	method to be used by splinefun
maxrfu	argument passed to baselineabif
...	arguments forwarded to 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.

Author(s)

J.R. Lobry

References

citation("seqinr")

See Also

function read.abif to import files in ABIF format, plotabif to plot them, data gs500liz for internal size standards, data identifiler for allele names in the allelic ladder, data JLO for an example of an individual sample file, data 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

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