Man pages for SimRVSequences
Simulate Genetic Sequence Data for Pedigrees
| affected_allele_count | Determine total number of alleles shared by affecteds in a... |
| affected_onlyPed | Remove unaffected relatives |
| assign_gen | Assign generation number based on oldest founder |
| check_ped | Checks individual pedigrees for proper format. |
| check_peds | Checks ped_files for expected info and format. |
| check_SNV_map | Check SNV_map for possible issues |
| combine_exons | Combine overlapping exons |
| combine_exons_by_chrom | Combine exons within a chromosome |
| combine_identicalmutations | Combine identical mutations |
| condition_haplos_no_cSNV | Reduce haplos to contain non-cSNV data |
| convert_BP_to_cM | Convert from basepairs to centimorgan |
| convert_CM_to_BP | Convert from centiMorgan to basepairs |
| create_chrom_map | Create chromosome map from marker map |
| create_slimMap | Create recombination map |
| EXhaps | Example Haplotypes dataset |
| EXmuts | Example Mutations dataset |
| extract_tempIDs | Determine i and j positions of mutations for sparse matrix |
| famStudy | Constructor function for an object of class famStudy |
| find_no_cSNV_rows | Find haplotypes that do not carry any cRVs |
| genos2sparseMatrix | Convert genotypes to haplotypes. |
| get_parOffInfo | Get parent and offspring information from a pedigree |
| get_SMindex_by_person | Returns the row and columns locations of mutations for a... |
| hg_apopPath | Apoptosis sub-pathway dataset |
| hg_exons | Human exon data |
| identify_pathwayRVs_byChrom | Identify variants located in a defined pathway |
| identify_pathwaySNVs | Identify SNVs located in a specified pathway |
| is.famStudy | Check to see if object is of class famStudy |
| is_int | Determine if input is an integer |
| is_odd | Determine if input is an odd number |
| is.SNVdata | Check to see if object is of class ped |
| load_1KG | Load pre-formatted 1000 Genomes Project exon data |
| read_slim | Import SLiM data to R |
| reconstruct_fromHaplotype | Construct offspring sequence from parental allele vector |
| reduce_to_events | Reduce chiasmata vector to crossovers that this gamete... |
| reMap_mutations | Re-map slim mutations |
| remove_allWild | Remove unmutated markers from data |
| resample | Dummy sample function |
| sim_chiasmataPositions | Simulate crossover positions |
| sim_FGenos | Draw Founder Genotypes from Haplotype Distribution Given... |
| sim_gameteFormation | Simulate formation of gametes. |
| sim_gameteInheritance | Simulate inheritance of parental gamete to offspring |
| sim_haploidFormation | Simulate recombination among chromatids. |
| sim_RVstudy | Simulate sequence data for a sample of pedigrees |
| sim_seq | Simulate sequence data for a pedigree |
| SNVdata | Constructor function for an object of class SNVdata |
| study_peds | Example pedigrees |
| summary.famStudy | Summary function for objects of class famStudy |
