haplo_selection: Generate a selection of markers appropriate for haplotype...

In malemay/HaplotypeMiner: Gene-centered haplotyping from SNP data

Generate a selection of markers appropriate for haplotype generation

Description

This function applies a series of filters on the genotype data provided (either in vcf or hapmap format) and outputs a list of markers kept at different stages of the analysis.

Usage

haplo_selection(analysis_parameters, snp_data = NULL, verbose = TRUE)

Arguments

analysis_parameters	a list of analysis parameters generated by the function build.analysis.parameters.
snp_data	To be completed.
verbose	To be completed.

Details

The behaviour of the function can be finely tuned by providing the function call with an analysis_parameters object with appropriate contents.

See function genotype.filter for a list of criteria used to filter the markers kept for haplotype generation.

So far, the function can only take hapmap and vcf files as input. The name of the input file must be provided in the list of analysis parameters, but there should also be an option allowing the user to provide a genotype object as input to this function. This would allow the user an easier way to look at their input data before carrying the analysis.

Value

A snp_data containing the subset of the chosen markers.

Examples

NULL

malemay/HaplotypeMiner documentation built on Feb. 6, 2024, 3:29 a.m.