Man pages for viewpoly
A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species
| breeding_values | Estimate breeding values - Adapted function from QTLpoly |
| calc_homologprob | Calculates homologues probabilities - Adapted from MAPpoly |
| check_viewmap | Viewmap object sanity check |
| check_viewpoly | Viewpoly object sanity check |
| check_viewqtl | viewqtl object sanity check |
| coord_radar | Change ggplot coordinates to plot radar - From package see |
| data_effects | Get effects information |
| dist_prob_to_class | Returns the class with the highest probability in a genotype... |
| draw_map_shiny | Draws linkage map, parents haplotypes and marker doses... |
| filter_non_conforming_classes | Filter non-conforming classes in F1, non double reduced... |
| get_LOD | Extract the LOD Scores in a "mappoly.map" object Function... |
| gg_color_hue | Color pallet ggplot-like - Adapted from MAPpoly |
| imf_h | Map functions - from MAPpoly |
| import_data_from_polymapR | Import data from polymapR |
| import_phased_maplist_from_polymapR | Import phased map list from polymapR |
| is.prob.data | Is it a probability dataset? Function from MAPpoly. |
| map_summary | Gets summary information from map. Adapted from MAPpoly |
| mf_h | Haldane map function. From MAPpoly |
| mrk_chisq_test | Chi-square test. Function from MAPpoly. |
| only_plot_profile | Only the plot part of plot_profile function |
| ph_list_to_matrix | Linkage phase format conversion: list to matrix. Function... |
| ph_matrix_to_list | Linkage phase format conversion: matrix to list. Function... |
| plot_cm_mb | Scatter plot relating linkage map and genomic positions |
| plot_effects | Plot effects data |
| plot_map_list | Plot a genetic map - Adapted from MAPpoly |
| plot.mappoly.homoprob | Plots mappoly.homoprob from MAPpoly |
| plot_one_map | Plot a single linkage group with no phase - from MAPpoly |
| plot_profile | Logarithm of _P_-value (LOP) profile plots. Modified version... |
| prepare_diaQTL | Converts diaQTL output to viewqtl object |
| prepare_examples | Upload example files |
| prepare_hidecan_examples | Upload hidecan example files |
| prepare_map | prepare maps for plot - from MAPpoly |
| prepare_map_custom_files | Converts map information in custom format files to viewmap... |
| prepare_MAPpoly | Converts list of mappoly.map object into viewmap object |
| prepare_polymapR | Converts polymapR ouputs to viewmap object |
| prepare_polyqtlR | Converts polyqtlR outputs to viewqtl object |
| prepare_qtl_custom_files | Converts QTL information in custom files to viewqtl object |
| prepare_QTLpoly | Converts QTLpoly outputs to viewqtl object |
| read_input_hidecan | Check hidecan inputs |
| run_app | Run the Shiny Application |
| segreg_poly | Polysomic segregation frequency - Function from MAPpoly |
| select_haplo | Plot selected haplotypes |
| summary_maps | Summary maps - adapted from MAPpoly |
