Man pages for malemay/HaplotypeMiner
Gene-centered haplotyping from SNP data
| cluster | Generate clusters of markers in high linkage disequilibrium |
| cluster_selection | Selecting marker clusters according to filtering criteria |
| compute_ld | Linkage disequilibrium computation |
| density_plot | Plot of marker density along chromosome |
| distance_plot | Plot of linkage disequilibrium as a function of the distance... |
| genotype_filter | Filter SNP data |
| genotype_plot | Title |
| gmgia_haplotypes | Analysis of gene _GmGia_ of soybean |
| haplo_graphs | Generate graphical output of a haplotype analysis |
| haplo_logfile | Generate the logfile of a haplotype analysis |
| haplo_output | Output the results of a haplotype analysis to disk |
| haplo_params | Title |
| haplo_selection | Generate a selection of markers appropriate for haplotype... |
| HaplotypeMiner | HaplotypeMiner: Gene-centered haplotyping from SNP data |
| haplotypes | Title |
| is_valid | Title |
| ld_plot | Generates a tile plot of the LD of the given snp_data. |
| mac | Title |
| marker_subset | Subsets a snp_data by keeping only certain markers. |
| r2expr | Convert r^2 measure into a printable expression |
| read_hapmap | Parse a hapmap file. |
| read_kinship | Title |
| read_structure | Title |
| read_vcf | Parse a vcf file. |
| restore_markers | Title |
| subcluster | Drop markers in perfect LD with adjacent markers, keeping... |
| write_hapmap | Export an snp_data into the hapmap format. |
| write_vcf | Write VCF output |
