R: Import GenMapper Panels configuration file

readPanels {seqinr} | R Documentation

## Import GenMapper Panels configuration file

### Description

In a Panel configuration file there is a description for a given identification kit of the marker names, their dye label color, expected size range, expected positive control genotypes, number of bases in core repeat, stutter percentages, and allele names.

### Usage

    readPanels(file,
      colnames = c("marker", "dye.col", "min.bp", "max.bp", "exp.pcg", "repeat.bp",
        "stutter.pc", "uknw", "allele names"))

### Arguments

`file` | The name of the Panel configuration file.
`colnames` | The names to be used for the columns of the data.frames.

### Details

Number of bases in core repeat is set to 9 for Amelogenin locus.

### Value

A list whose first element is the file header info and following elements data.frames, one for each kit encountered in the file.

### Author(s)

J.R. Lobry

### References

`citation("seqinR")`

### See Also

`readBins`, `plotPanels`.

### Examples

    #
    # Check that we can read the 2 exemple files in the seqinR package:
    #
    path1 <- system.file("abif/AmpFLSTR_Panels_v1.txt", package = "seqinr")
    res1 <- readPanels(path1)
    path2 <- system.file("abif/Promega_Panels_v1.txt", package = "seqinr")
    res2 <- readPanels(path2)
    #
    # Show the kits described in res1:
    #
    names(res1)
    #
    # Show some data for a given kit:
    #
    res1[["Identifiler_v1"]][, 1:7]
    #
    # Plot a simple summary of two kits:
    #
    par(mfrow = c(2,1))
    plotPanels("Identifiler_v1", res1)
    plotPanels("PowerPlex_16_v1", res2)

    #
    # Simple quality check since seqinR 2.0-4 with a file which containing
    # a non constant number of tabulations as separator:
    #
    path3 <- system.file("abif/Prototype_PowerPlex_EP01_Pa.txt", package = "seqinr")
    res3 <- readPanels(path3)

[Package seqinr version 3.4-5 Index]