readHapMap: Reading SNP data from the HapMap consortium

Description

This function reads HapMap data.

Usage

readHapMap(folder,hap_gffpath,populations=FALSE,outgroup=FALSE)

Arguments

folder

the basepath of the variant_calls

hap_gffpath

the basepath of the corresponding gff-files. Note! This gff_file does not contain information about subsites. see details!

populations

list of populations

outgroup

vector of outgroup sequences

Value

The function creates an object of class "GENOME" --------------------------------------------------------- Following Slots will be filled in the "GENOME" object --------------------------------------------------------- rll{ Slot Description 1. n.sites total number of sites 2. n.biallelic.sites number of biallelic sites 3. region.data some detail data informations }

Details

PopGenome reads the gff file distributed on the HapMap plattform only to verify the reference positions of the chromosomes. In the next release this function will also handle GFF/GTF files to get informations about subsites like exons and so on. The folder includes the files of different individuals of one chromosome. This enables also FST calculations of the HapMap data.

Examples

Run this code

# GENOME.class <- readHapMap("...\HapMapData")
# GENOME.class
# show the result:
# get.sum.data(GENOME.class)
# GENOME.class@region.data

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