readHapMap: Read SNP data from the HapMap consortium

In PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

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! 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

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

PopGenome documentation built on Feb. 1, 2020, 1:07 a.m.