Man pages for simrvprojects/SimRVSequences
Simulate Genetic Sequence Data for Pedigrees

affected_allele_countDetermine total number of alleles shared by affecteds in a...
affected_onlyPedRemove unaffected relatives
assign_genAssign generation number based on oldest founder
check_pedChecks individual pedigrees for proper format.
check_pedsChecks ped_files for expected info and format.
check_SNV_mapCheck SNV_map for possible issues
combine_exonsCombine overlapping exons
combine_exons_by_chromCombine exons within a chromosome
combine_identicalmutationsCombine identical mutations
condition_haplos_no_cSNVReduce haplos to contain non-cSNV data
convert_BP_to_cMConvert from basepairs to centimorgan
convert_CM_to_BPConvert from centiMorgan to basepairs
create_chrom_mapCreate chromosome map from marker map
create_slimMapCreate recombination map
EXhapsExample Haplotypes dataset
EXmutsExample Mutations dataset
extract_tempIDsDetermine i and j positions of mutations for sparse matrix
famStudyConstructor function for an object of class famStudy
find_no_cSNV_rowsFind haplotypes that do not carry any cRVs
genos2sparseMatrixConvert genotypes to haplotypes.
get_parOffInfoGet parent and offspring information from a pedigree
get_SMindex_by_personReturns the row and columns locations of mutations for a...
hg_apopPathApoptosis sub-pathway dataset
hg_exonsHuman exon data
identify_pathwayRVs_byChromIdentify variants located in a defined pathway
identify_pathwaySNVsIdentify SNVs located in a specified pathway
is.famStudyCheck to see if object is of class famStudy
is_intDetermine if input is an integer
is_oddDetermine if input is an odd number
is.SNVdataCheck to see if object is of class ped
load_1KGLoad pre-formatted 1000 Genomes Project exon data
read_slimImport SLiM data to R
reconstruct_fromHaplotypeConstruct offspring sequence from parental allele vector
reduce_to_eventsReduce chiasmata vector to crossovers that this gamete...
reMap_mutationsRe-map slim mutations
remove_allWildRemove unmutated markers from data
resampleDummy sample function
sim_chiasmataPositionsSimulate crossover positions
sim_FGenosDraw Founder Genotypes from Haplotype Distribution Given...
sim_gameteFormationSimulate formation of gametes.
sim_gameteInheritanceSimulate inheritance of parental gamete to offspring
sim_haploidFormationSimulate recombination among chromatids.
sim_RVstudySimulate sequence data for a sample of pedigrees
sim_seqSimulate sequence data for a pedigree
SNVdataConstructor function for an object of class SNVdata
study_pedsExample pedigrees
summary.famStudySummary function for objects of class famStudy
simrvprojects/SimRVSequences documentation built on Dec. 8, 2019, 4:12 p.m.