SimRVPedigree (version 0.4.4)

new.ped: Create an object of class ped.

Description

Create an object of class ped, from a data.frame, required input for reassign_gen, censor_ped, and trim_ped functions.

Usage

new.ped(ped_file)

Arguments

ped_file

Data.frame. A pedigree, see details.

Value

An object of class ped.

Details

The data frame supplied to new.ped, ped_file, must contain the following variables:

name	type	description
FamID	numeric	family identification number
ID	numeric	individual identification number
dadID	numeric	identification number of father
momID	numeric	identification number of mother
sex	numeric	gender identification; if male sex = 0, if female sex = 1
affected	logical	disease-affection status:
		affected = TRUE if affected by disease, and FALSE otherwise,

Optionally, ped_file may contain any of the following variables:

name	type	description
available	logical	availibility status;
		available = TRUE if available, and FALSE otherwise.
DA1	numeric	paternally inherited allele at the assumed disease locus:
		DA1 = 1 if rare variant is present, and 0 otherwise
DA2	numeric	maternally inherited allele at the assumed disease locus:
		DA2 = 1 if rare variant is present, and 0 otherwise
birthYr	numeric	the individual's birth year
onsetYr	numeric	the individual's year of disease onset, when applicable, otherwise NA
deathYr	numeric	the individual's year of death, when applicable, otherwise NA
RR	numeric	the individual's relative-risk of disease
Gen	numeric	the individual's generation number relative to the eldest founder.
		For the eldest founder Gen = 1, for his or her offspring Gen = 2, etc.
proband	logical	proband identifier:
		proband = TRUE if individual is the proband, and FALSE otherwise.
subtype	character	the individual's disease subtype, when applicable, otherwise NA

We note that some of the optional fields above may be required for various ped functions

Examples

# NOT RUN {
data(EgPeds)
head(EgPeds)

ped1 = new.ped(EgPeds[EgPeds$FamID == 1, ])
head(ped1, n = 3)
class(ped1)
summary(ped1)

AllPeds = new.ped(EgPeds)
head(AllPeds)
class(AllPeds)
summary(AllPeds)

# }