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

Run this code

# 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)

# }