Package index • gwid

All functions

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