Description Usage Arguments Details Value Examples
Summarize a sample of pedigrees
1 2 |
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. | |
|
A data frame containing family specific variables for each pedigree supplied. See details. |
|
A data frame containing information for the affected individuals in each pedigree supplied. See details. |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | #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)
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