readHapMap: Read SNP data from the HapMap consortium

Description Usage Arguments Details Value Examples

Description

This function reads HapMap data.

Usage

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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! The HapMap GFF file does not contain information about subsites. see details!

populations

list of populations

outgroup

vector of outgroup sequences

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 information about subsites (exons, introns, ...). The input folder should include the files of different individuals for one chromosome. This facilitates FST calculations of the HapMap data.
See also readData("...", format="HapMap") which can read the files of single populations directly.

Value

The function creates an object of class "GENOME"

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The following slots will be filled in the "GENOME" object
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Slot Description
1. n.sites total number of sites
2. n.biallelic.sites number of biallelic sites
3. region.data some detailed information about the data read

Examples

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# GENOME.class <- readHapMap("...\HapMapData")
# GENOME.class
# show the result:
# get.sum.data(GENOME.class)
# [email protected]

pievos101/PopGenome documentation built on May 16, 2019, 2:54 a.m.