# Genome-Wide Identity-by-Descent

## Documentation for package ‘gwid’ version 0.3.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

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