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... |
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_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... |
launch_app | laucnh a shiny app |
mcnemar_test | mcnemar test |
mcnemar_test_permut | mcnemar permutation |
mcnemar_test_permut.result_snps | mcnemar permutation test |
mcnemar_test.result_snps | mcnemar 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... |
plot.result_snps | Line plot of result_snps objects |
plot.test_snps | Line plot of test_snps objects |
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 |
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