plotladder: Simple plot of an allelic ladder from ABIF data

In seqinr: Biological Sequences Retrieval and Analysis

Simple plot of an allelic ladder from ABIF data

Description

Simple representation of an observed allelic ladder.

Usage

plotladder(abifdata, chanel, calibr, allele.names = "identifiler", npeak = NULL, ...)

Arguments

abifdata	the result returned by read.abif
chanel	the dye number
calibr	a mandatory calibration function to convert time into bp
allele.names	name of the dataset which contains allele names as in link{identifiler}
npeak	expected number of peaks, deduced from allele.names by default
...	arguments forwarded to peakabif

Value

Returns invisibly the location of peaks in bp.

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

  #
  # load an example of allelic ladder results from an ABIF (*.fsa) file:
  #
data(ECH)
  #
  # Extract from internal size standard chanel number 5 the location 
  # of 14 peaks:
  #
ECH.maxis <- peakabif(ECH, 5, npeak = 14, tmin = 2.7, thres = 0.1, fig = FALSE)$maxis
  #
  # Load data about the expected size of peaks in bp for calibration:
  #
data(gs500liz)
lizbp <- gs500liz$liz # All peaks size in bp
lizbp[!gs500liz$mask1 | !gs500liz$mask2] <- NA # Mark useless peaks
lizbp <- lizbp[-c(1,2)] # The first two peaks are not extracted from ECH
ECH.calibr <- splinefun(ECH.maxis[!is.na(lizbp)], lizbp[!is.na(lizbp)])
  #
  # Show the allelic ladder for the 4 dyes:
  #
plotladder(ECH, 1, ECH.calibr, tmin = 3.1, thres = 0.3, fig = FALSE)
plotladder(ECH, 2, ECH.calibr, tmin = 3.1, thres = 0.35, fig = FALSE)
plotladder(ECH, 3, ECH.calibr, tmin = 3.1, thres = 0.2, fig = FALSE)
plotladder(ECH, 4, ECH.calibr, tmin = 3.1, thres = 0.2, fig = FALSE)

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