build_gwas              Open a SNP GDS file and extract information.
build_gwid              Open a ibd file and extract information.
build_phase             Read .vcf structured text format files and
                        reduce the size of file.
case_control            Reload saved case-control list file
extract                 Extract information from SNP GDS file.
extract.gwas            Extract information from SNP GDS file.
extract.gwid            Extract information from ibd data.
extract_window          extract component of an object
extract_window.gwid     Extract information from ibd data in a moving
                        window
fisher_test             Fisher test
fisher_test.gwas        Fisher's Exact Test for gwas count data
fisher_test.gwid        Fisher's Exact Test for gwid count data
fisher_test.result_snps
                        fisher exact test for result_snps count data
gtest                   perform gtest
gtest.haplotype_structure
                        Perform G-test on haplotype structures
                        extracted from 'haplotype_structure' function
haplotype_frequency     haplotype frequency
haplotype_frequency.haplotype_structure
                        haplotype frequency in sliding windows
haplotype_structure     haplotype structures in a window
haplotype_structure.gwas
                        extract haplotype structures of individuals in
                        a window
haplotype_structure.gwid
                        extract haplotype structures of pairwise ibd
                        samples in a window
launch_app              laucnh a shiny app
mcnemar_test            mcnemar test
mcnemar_test.result_snps
                        mcnemar test
mcnemar_test_permut     mcnemar permutation
mcnemar_test_permut.result_snps
                        mcnemar permutation test
permutation_test        permutation test
permutation_test.gwas   Permutation test for gwas object
permutation_test.gwid   permutation test for gwid count data
permutation_test.haplotype_structure
                        Permutation test for 'haplotype_structure'
                        object
plot.gwas               Line plot of gwas objects
plot.gwid               Line plot of gwid objects
plot.haplotype_frequency
                        Line plot of haplotype_frequency object
plot.haplotype_structure_frequency
                        Two type of line plots for
                        haplotype_structure_frequency objects .
plot.result_snps        Line plot of result_snps objects
plot.test_snps          Line plot of test_snps objects
print                   print
print.gwas              print gwas instants
roh                     runs of homozygosity
roh.phase               runs of homozygosity
subset                  subset an object
subset.gwid             subset gwid object based on snp position
