SimRVPedigree (version 0.4.4)

summary.ped: Summarize a sample of pedigrees

Description

Summarize a sample of pedigrees

Usage

# S3 method for ped
summary(object, ...)

Arguments

object

An object of class ped.

...

additional arguments passed to other methods.

Value

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.

Details

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.

Examples

# NOT RUN {
#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)

# }