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"
———————————————————
The following slots will be filled in the "GENOME" object
———————————————————
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)
# GENOME.class@region.data