Learn R Programming
⚠️There's a newer version (0.4.4) of this package.Take me there.

SimRVPedigree (version 0.3.0)

Simulate Pedigrees Ascertained for a Rare Disease

Description

Routines to simulate and manipulate pedigrees ascertained to contain multiple family members affected by a rare disease. Christina Nieuwoudt, Samantha J Jones, Angela Brooks-Wilson, and Jinko Graham (2018) .

Copy Link

Version

Install

install.packages('SimRVPedigree')

Monthly Downloads

20

Version

0.3.0

License

GNU General Public License

Maintainer

Christina Nieuwoudt

Last Published

October 1st, 2018

Functions in SimRVPedigree (0.3.0)

create_pedFile

Create an empty pedigree
get_kinship

Compute kinship matrix for the affected relatives
sim_ped

Simulate a pedigree
get_wait_time

obtain the waiting time to the next event
sim_nFam

Simulate a nuclear family from a single founder
get_famInfo

Obtain summary information
get_wait_prob

Obtain the cumulative probability of the waiting time to the next event
get_gen_labs

Get generation lables
find_missing_parent

Find parents that have been removed but are required for plotting.
find_available_parent

Find available parent
disqualify_ped

Initial checks to disqualify a pedigree from ascertainment.
hazard

Create an object of class hazard.
create_mate

Create a new mate
sim_founderRVstatus

Determine founder genotype at the disease locus and determime their relative-risk of disease
get_nextEvent

Simulate the next life event
is.ped

Check to see if object is of class ped
new.ped

Create an object of class ped.
plot.ped

Plot pedigree
create_offspring

Create a new offspring
pedigreeLabels

Create pedigree labels
is.hazard

Check to see if object is of class hazard
EgPeds

Example pedigrees
sim_life

Simulate all life events
reassign_gen

Reassign generation number based on affected status
sim_RVped

Simulate a pedigree ascertained to contain multiple disease-affected relatives
find_mrca

Find the most recent common ancestor of two pedigree members
get_affectedInfo

Gather information for the affected relatives
ped

Constructor function for an object of class ped
ped2pedigree

Create a kinship2 pedigree structure from an object of class ped
summary.ped

Summarize a sample of pedigrees
trim_ped

Trim pedigree based on proband recall
SimRVPedigree

Simulate pedigrees ascertained for disease status
ascertainTrim_ped

Check to see if a trimmed pedigree is ascertained.
create_founder

Create a new seed founder
choose_proband

Choose a proband from the disease-affected relatives in a pedigree
censor_ped

Censor pedigree data
check_ped

Checks ped_file for expected information, used before converting to ped object.
ascertain_ped

Determine if a pedigree is ascertained
AgeSpecific_Hazards

Age-specific hazard rate dataset
assign_gen

Assign generation number based on oldest founder