summary.ped: Summarize a sample of pedigrees
In SimRVPedigree: Simulate Pedigrees Ascertained for a Rare Disease

Description Usage Arguments Details Value Examples

Summarize a sample of pedigrees

1 2	## S3 method for class 'ped' summary(object, ...)

`object`	An object of class ped.
`...`	additional arguments passed to other methods.

The summary.ped function returns two data frames. The first is called family_info, and contains the following fields for each family supplied.

variable	description
`FamID`	family identification number
`totalRelatives`	total number of relatives
`numAffected`	total number of disease-affected individuals
`aveOnsetAge`	average onset age among the disease-affected relatives
`aveIBD`	average of the pairwise IBD probabilities among the disease-affected relatives
`ascertainYear`	the year the pedigree was ascertained
`segRV`	logical Indicates whether or not pedigree segregates a causal variant.
	If the pedigree segregates the variant `segRV = TRUE`.
`p_subtypeLabel`	NOTE: this is only listed when pedigrees contain relatives affected by multiple subtypes.
	the proportion of disease-affected relatives in the family with the specified subtype.
	Here "subtypeLabel" is determined by subtype ID specifed by the user when creating the
	`hazard` object.

The second item returned by summary.ped is called affected_info, and contains the following fields for each disease-affected relative supplied.

variable	description
`FamID`	family identification number
`ID`	individual identification number
`birthYr`	the individual's birth year, when applicable, otherwise `NA`
`onsetYr`	the individual's year of disease onset, when applicable, otherwise `NA`
`deathYr`	the individual's year of death, when applicable, otherwise `NA`
`proband`	a proband identifier: `proband = TRUE` if the individual is the proband, and `FALSE` otherwise.
`RVstatus`	the individual's causal RV status; set to 1 if individual is a carrier, and 0 otherwise.
`subtype`	NOTE: this is only listed when pedigree was simulated for diseases with multiple subtypes.
	The individual's disease subtype.

`family_info`	A data frame containing family specific variables for each pedigree supplied. See details.
`affected_info`	A data frame containing information for the affected individuals in each pedigree supplied. See details.

#Read in age-specific harard data and create hazard object.
data(AgeSpecific_Hazards)
haz_obj <- hazard(hazardDF = AgeSpecific_Hazards)

#Simulate a pedigree ascertained for multiple affecteds
set.seed(6)
RVped2015 <- sim_RVped(hazard_rates = haz_obj,
                       num_affected = 2,
                       ascertain_span = c(1900, 2015),
                       GRR = 30, carrier_prob = 0.002,
                       RVfounder = TRUE,
                       stop_year = 2015,
                       recall_probs = c(1),
                       founder_byears = c(1900, 1925),
                       FamID = 1)[[2]]

# Plot the pedigree with age labels at the year 2015
plot(RVped2015, ref_year = 2015)

# View summary information for the pedigree
summary(RVped2015)



# Import the EgPeds dataset and create ped object
data(EgPeds)
study_peds <- new.ped(EgPeds)

# View summary information for study_peds
summary(study_peds)