Fluidigm (version 0.2)

getPairwiseSimilarityLoci: Get Pairwise Similarity Loci

Description

This function is a wrapper to a perl script that determines the loci of pairwise similarities. It is designed to work with data from the 'PLINK' software, which is commonly used in bioinformatics for whole genome association analysis.

Usage

getPairwiseSimilarityLoci(file, verbose = TRUE, verbosity = 1)

Value

This function does not return a value in the R environment. Instead, it creates an output file with the '.pairs' extension in the same directory as the input file. This output file contains the results of the pairwise similarity loci analysis.

Arguments

file

A string. This is the path to the previously created PLINK ped file (with .ped extension). The ped file contains genotype information in a format that can be used for further analysis.

verbose

A logical. If TRUE, the function will print detailed messages during its execution to help you understand what it's doing at each step. Default is TRUE.

verbosity

An integer. This parameter controls the level of verbosity. The higher the number, the more detailed the messages. Default is 1.

Details

This function first checks the input parameters. It then constructs the output file names and the command to run the perl script. The command is executed using the system function. If the 'verbose' parameter is set to TRUE, the function will print a message when it has finished running.

The perl script was written by Doug Scofield, see references.

References

The original code this function is based on can be found at: GitHub https://github.com/douglasgscofield/bioinfo/blob/main/scripts/plink-pairwise-loci.pl

Examples

if (FALSE) {
  outdir <- tempdir()
  getPairwiseSimilarityLoci(file = file.path(outdir, "example_data.csv.GOOD"))
}