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 |