readPanels: Import GenMapper Panels configuration file

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/readPanels.R

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

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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

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#
# 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)

seqinr documentation built on June 9, 2021, 9:06 a.m.