haplo_output: Output the results of a haplotype analysis to disk
In malemay/HaplotypeMiner: Gene-centered haplotyping from SNP data

haplo_output

R Documentation

Output the results of a haplotype analysis to disk

Description

This function takes an object returned by function haplo_selection as input and extracts information from this object so as the make the information easily interpretable by the user. The function directs the output of essentially three elements : the analysis logfile, the variant files (vcf or hapmap) containing the marker set at different steps of the analysis, and various kinds of graphs

Usage

haplo_output(results, output_dir = NULL, logfile = "Log.txt",
  variant_files = "default",
  variant_format = results$Parameters$File_format, graphs = "default")

Arguments

`results`	A list generated as output from the function `haplo_selection` and thus containing the results of a haplotype analysis.
`output_dir`	A list generated as output from the function `haplo_selection` and thus containing the results of a haplotype analysis.
`logfile`	A character. The name of the file to which the logfile should be written. Defaults to "Log.txt". If `NULL`, no logfile is written.
`variant_files`	A character vector. The name of the list elements of `results` that should used to output the variant data to disk. Can be any of `All_markers`, `Filtered_markers`, `Clustered_markers`, `Selected_clusters`, `Selected_markers`, `Haplotypes`. Defaults to the last three of these elements. If null, no variant file will be written to disk.
`variant_format`	A character. The format to be used for writing variant files. Must be either "vcf" or "hapmap". Other formats are not supported and will result in an error.
`graphs`	A list describing which graphical elements should be output. See `haplo_graphs` for more details.

Details

More control over the files output by this function can be obtained by using the underlying functions : haplo_logfile, haplo_graphs, write_hapmap