readBins: Import GenMapper Bins configuration file

Description

In a Bins configuration file there is a description for a given identification kit of the expected allele sizes for all the markers available in the kit.

Usage

readBins(file, 
  colnames = c("allele.name", "size.bp", "minus.bp", "plus.bp"))

Arguments

file

The name of the Bins configuration file.

colnames

The names to be used for the columns of the data.frames.

Value

A list whose first element is the file header info and following elements are lists, one for each kit encountered in the file. For each kit we have a list of data.frames, one per marker.

Details

The expected allele sizes are typically plus or minus 0.5 bp.

References

citation("seqinR")

Examples

Run this code

# NOT RUN {
#
# Check that we can read the 2 exemple files in the seqinR package:
#
path1 <- system.file("abif/AmpFLSTR_Bins_v1.txt", package = "seqinr")
resbin1 <- readBins(path1)
path2 <- system.file("abif/Promega_Bins_v1.txt", package = "seqinr")
resbin2 <- readBins(path2)
#
# Show the kits described in resbin1:
#
names(resbin1)
#
# Show the markers in a given kit:
#
names(resbin1[["Identifiler_v1"]])
#
# Show alleles expected sizes for a given marker:
#
resbin1[["Identifiler_v1"]][["D8S1179"]]
#
# Simple quality check since seqinr 2.0-4 with a configuration file
# containing trailling tabulations:
#
path3 <- system.file("abif/Prototype_PowerPlex_EP01_Bins.txt", package = "seqinr")
resbin3 <- readBins(path3)
ncols <- sapply(resbin3[[2]], ncol)
stopifnot(all(ncols == 4))
# }

Run the code above in your browser using DataCamp Workspace