seqinr (version 3.4-5)

peakabif: 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.

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

# NOT RUN {
data(JLO)
JLO.maxis <- peakabif(JLO, 5, npeak = 14, tmin = 2.7, thres = 0.1)$maxis
# }