haplo_logfile: Generate the logfile of a haplotype analysis
In malemay/HaplotypeMiner: Gene-centered haplotyping from SNP data

Description Usage Arguments Details Value Examples

This function inspects the output of the haplo_selection function in order to generate a logfile summarizing details of the analysis. The logfile can be output to a file (defaults to "Log.txt") or to optionally to standard output.

1	haplo_logfile(results, filename = "Log.txt", to_file = TRUE)

`results`	A list containing a variable number of items among the following : `Parameters`, `Kinship`, `Structure`, `All_markers`, `Filtered_markers`, `Clustered_markers`, `Selected_clusters`, `Selected_markers`, `Haplotypes`. The precise output of the function will depend on the number of these elements given as input. The function will throw an error if any element other than those aforementioned is present in the input list.
`filename`	A character. The name of the file to which the logfile should be written. Ignored if `to_file` is FALSE.
`to_file`	A logical. Should the output be written to file? Defaults to TRUE, otherwise output is directed to standard output.

The logfile is divided into 4 parts :

Analysis parameters A description of the input files and parameters that were used for the analysis.
Marker clustering and filtering results A description of the number of markers that were kept following different filtering steps.
Selecting marker pairs in LD across gene Data regarding the final set of markers kept for haplotype generation.
Haplotype assignment A summary of the number of different haplotypes generated and the number of individuals unambiguously assigned to each haplotype, plus the number of individuals that could not be unambiguously assigned to a haplotype due to missing data.

NULL, invisibly. This function is called for its side effect of writing to file or to standard output.