Genome-Wide Identity-by-Descent
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Documentation for package ‘gwid’ version 0.1.0
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 |
| 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.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 |