R: Import GenMapper Bins configuration file

readBins {seqinr} | R Documentation

## 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))

[Package seqinr version 3.4-5 Index]