readBins: Import GenMapper Bins configuration file

In seqinr: Biological Sequences Retrieval and Analysis

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.

Details

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

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.

Author(s)

J.R. Lobry

References

citation("seqinR")

See Also

readPanels.

Examples

#
# 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))

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