R: Simple plot of an allelic ladder from ABIF data

plotladder {seqinr} | R Documentation

## 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)

[Package seqinr version 3.4-5 Index]