Man pages for onemap
Construction of Genetic Maps in Experimental Crosses
| acum | Perform gaussian sum |
| add_marker | Creates a new sequence by adding markers. |
| add_redundants | Add the redundant markers removed by create_data_bins... |
| Bonferroni_alpha | Calculates individual significance level to be used to... |
| check_data | Onemap object sanity check |
| check_twopts | Twopts object sanity check |
| combine_onemap | Combine OneMap datasets |
| compare | Compare all possible orders (exhaustive search) for a given... |
| create_data_bins | New dataset based on bins |
| create_dataframe_for_plot_outcross | Create a dataframe suitable for a ggplot2 graphic |
| create_depths_profile | Create database and ggplot graphic of allele reads depths |
| create_probs | Build genotype probabilities matrix for hmm |
| draw_map | Draw a genetic map |
| draw_map2 | Draw a linkage map |
| drop_marker | Creates a new sequence by dropping markers. |
| empty_onemap_obj | Produce empty object to avoid code break. Function for... |
| est_map_hmm_out | C++ routine for multipoint analysis in outcrossing... |
| extract_depth | Extract allele counts of progeny and parents of vcf file |
| filter_2pts_gaps | Filter markers based on 2pts distance |
| filter_missing | Filter markers according with a missing data threshold |
| filter_prob | Function filter genotypes by genotype probability |
| find_bins | Allocate markers into bins |
| generate_overlapping_batches | Function to divide the sequence in batches with user defined... |
| group | Assign markers to linkage groups |
| group_seq | Assign markers to preexisting linkage groups |
| group_upgma | Assign markers to linkage groups |
| haldane | Apply Haldane mapping function |
| keep_only_selected_mks | Keep in the onemap and twopts object only markers in the... |
| kosambi | Apply Kosambi mapping function |
| make_seq | Create a sequence of markers based on other OneMap object... |
| map | Construct the linkage map for a sequence of markers |
| map_avoid_unlinked | Repeat HMM if map find unlinked marker |
| mapmaker_example_f2 | Simulated data from a F2 population |
| map_overlapping_batches | Mapping overlapping batches |
| map_save_ram | Perform map using background objects with only selected... |
| marker_type | Informs the segregation patterns of markers |
| mds_onemap | OneMap interface with MDSMap package with option for... |
| onemap_example_bc | Simulated data from a backcross population |
| onemap_example_f2 | Simulated data from a F2 population |
| onemap_example_out | Data from a full-sib family derived from two outbred parents |
| onemap_example_riself | Simulated data from a RIL population produced by selfing. |
| onemap_read_vcfR | Convert vcf file to onemap object |
| order_seq | Search for the best order of markers combining compare and... |
| parents_haplotypes | Generates data.frame with parents estimated haplotypes |
| pick_batch_sizes | Picking optimal batch size values |
| plot_by_segreg_type | Draw a graphic showing the number of markers of each... |
| plot.group.upgma | Show the results of grouping procedure |
| plot.onemap | Draw a graphic of raw data for any OneMap population |
| plot.onemap_progeny_haplotypes | Plots progeny haplotypes |
| plot.onemap_progeny_haplotypes_counts | Plot recombination breakpoints counts for each individual |
| plot.onemap_segreg_test | Plot p-values for chi-square tests of expected segregation |
| print.compare | print method for object class 'compare' |
| print.group | Show the results of grouping procedure |
| print.group_seq | Show the results of grouping markers to preexisting sequence |
| print.group.upgma | Show the results of grouping procedure |
| print.onemap | Print method for object class 'onemap' |
| print.onemap_bin | print method for object class 'onemap_bin' |
| print.onemap_segreg_test | Show the results of segregation tests |
| print.order | Print order_seq object |
| print.rf_2pts | Print method for object class 'rf_2pts' |
| print.sequence | Print method for object class 'sequence' |
| print.try | Print method for object class 'try' |
| progeny_haplotypes | Generate data.frame with genotypes estimated by HMM and its... |
| progeny_haplotypes_counts | Plot number of breakpoints by individuals |
| rcd | Rapid Chain Delineation |
| read_mapmaker | Read data from a Mapmaker raw file |
| read_onemap | Read data from all types of progenies supported by OneMap |
| record | Recombination Counting and Ordering |
| remove_inds | Remove individuals from the onemap object |
| rf_2pts | Two-point analysis between genetic markers |
| rf_graph_table | Plots pairwise recombination fractions and LOD Scores in a... |
| rf_snp_filter_onemap | Filter markers according with a two-points recombination... |
| ripple_seq | Compares and displays plausible alternative orders for a... |
| rm_dupli_mks | Remove duplicated markers keeping the one with less missing... |
| seeded_map | Construct the linkage map for a sequence of markers after... |
| select_segreg | Show markers with/without segregation distortion |
| seq_by_type | Extract marker number by name |
| seriation | Seriation |
| set_map_fun | Defines the default mapping function |
| sort_by_pos | Sort markers in onemap object by their position in reference... |
| split_2pts | Split rf_2pts object by markers |
| split_onemap | Split onemap data sets |
| suggest_lod | Suggests a LOD Score for two point tests |
| test_segregation | test_segregation |
| test_segregation_of_a_marker | test_segregation_of_a_marker |
| try_seq | Try to map a marker into every possible position between... |
| try_seq_by_seq | Run try_seq considering previous sequence |
| ug | Unidirectional Growth |
| vcf2raw | These functions are defunct and no longer available. |
| vcf_example_bc | Data generated from VCF file with biallelic markers from a f2... |
| vcf_example_f2 | Data generated from VCF file with biallelic markers from a f2... |
| vcf_example_out | Data generated from VCF file with biallelic markers from a... |
| vcf_example_riself | Data generated from VCF file with biallelic markers from a... |
| write_map | Write a genetic map to a file |
| write_onemap_raw | Convert onemap object to onemap raw file |
