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SimRVSequences

SimRVSequences provides routines to simulate single nucleotide variant (SNV) data for pedigrees.

Installation

You can install SimRVSequences from github with:

# install.packages("devtools")
devtools::install_github("cnieuwoudt/SimRVSequences")

News

We are pleased to announce that SimRVSequences (>= 0.2.0) features pre-formatted, exon-only SNV data from the 1000 Genomes Project.

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Version

Install

install.packages('SimRVSequences')

Monthly Downloads

30

Version

0.2.7

License

GNU General Public License

Maintainer

Christina Nieuwoudt

Last Published

June 29th, 2020

Functions in SimRVSequences (0.2.7)

condition_haplos_no_cSNV

Reduce haplos to contain non-cSNV data

Human exon data

convert_BP_to_cM

Convert from basepairs to centimorgan

create_chrom_map

Create chromosome map from marker map

identify_pathwayRVs_byChrom

Identify variants located in a defined pathway

combine_exons_by_chrom

Combine exons within a chromosome

Create recombination map

identify_pathwaySNVs

Identify SNVs located in a specified pathway

combine_identicalmutations

Combine identical mutations

convert_CM_to_BP

Convert from centiMorgan to basepairs

Get parent and offspring information from a pedigree

reconstruct_fromHaplotype

Construct offspring sequence from parental allele vector

Check to see if object is of class ped

Determine if input is an odd number

reduce_to_events

Reduce chiasmata vector to crossovers that this gamete participated in based on the allele vector.

Apoptosis sub-pathway dataset

Constructor function for an object of class famStudy

genos2sparseMatrix

Convert genotypes to haplotypes.

find_no_cSNV_rows

Find haplotypes that do not carry any cRVs

extract_tempIDs

Determine i and j positions of mutations for sparse matrix

Load pre-formatted 1000 Genomes Project exon data

sim_gameteInheritance

Simulate inheritance of parental gamete to offspring

sim_haploidFormation

Simulate recombination among chromatids.

Checks individual pedigrees for proper format.

Simulate sequence data for a sample of pedigrees

Draw Founder Genotypes from Haplotype Distribution Given Familial Risk Variant

reMap_mutations

Re-map slim mutations

get_SMindex_by_person

Returns the row and columns locations of mutations for a person

sim_gameteFormation

Simulate formation of gametes.

sim_chiasmataPositions

Simulate crossover positions

Check to see if object is of class famStudy

Determine if input is an integer

Remove unmutated markers from data

Simulate sequence data for a pedigree

Dummy sample function

Import SLiM data to R

summary.famStudy

Summary function for objects of class famStudy

Example pedigrees

Constructor function for an object of class SNVdata

Example Mutations dataset

Combine overlapping exons

affected_onlyPed

Remove unaffected relatives

Check SNV_map for possible issues

Checks ped_files for expected info and format.

Assign generation number based on oldest founder

affected_allele_count

Determine total number of alleles shared by affecteds in a family

Example Haplotypes dataset