summary.famStudy: Summary function for objects of class famStudy

In SimRVSequences: Simulate Genetic Sequence Data for Pedigrees

Description

Summary function for objects of class famStudy, i.e. objects returned by the sim_RVstudy function.

Usage

## S3 method for class 'famStudy'
summary(object, ...)

Arguments

object	An object of class famStudy, returned by the sim_RVstudy function.
...	additional arguments passed to other methods.

Details

The summary.famStudy function returns a list containing two items. The first item, fam_allele _count, is a matrix that contains counts of the SNVs shared by the disease-affected relatives in each pedigree. This matrix will contain a row of counts for each pedigree in the supplied famSutdy object. The first column in fam_allele_count is named FamID and identifies each pedigree by their family identification number. The remaining columns in fam_allele_count are named according to the respective marker names of the shared SNVs.

The second item returned by summary.famStudy is a data frame named pathway_count, which catalogs the SNVs shared among disease-affected study participants. This data frame contains the following variables:

name	type	description
chrom	numeric	chromosome identification number
position	numeric	the position of the SNV
marker	character	a unique character identifier for the SNV
total	numeric	the number of SNV copies observed in disease-affected study participants.
is_crv	logical	identifies causal rare variants (cRVs) as TRUE
pathwaySNV	logical	identifies SNVs located within the pathway of interest as TRUE.

Please note, the variable pathwaySNV is omitted when missing from the SNV_map data frame in the famStudy object. See sim_RVstudy for more details.

Value

fam_allele_count	A matrix that contains counts of the SNVs shared by the disease-affected relatives in each pedigree.
pathway_count	A data frame that catalogs the SNVs shared among disease-affected study participants. See details.

See Also

sim_RVstudy

Examples

library(SimRVSequences)

# load pedigree, haplotype, and mutation data
data(study_peds)
data(EXmuts)
data(EXhaps)

# create variable is_CRV in EXmuts to identify the causal
# rare variants from which to sample familial cRVs.
EXmuts$is_CRV = FALSE
EXmuts$is_CRV[c(26, 139, 223, 228, 472)] = TRUE

# supply required inputs to the sim_RVstudy function
seqDat = sim_RVstudy(ped_files = study_peds,
                     SNV_data = SNVdata(Haplotypes = EXhaps,
                                        Mutations = EXmuts))

# to count the number of SNVs shared by the disease-affected
# relatives in each pedigree, supply the output returned by
# sim_RVstudy to the summary function
summary(seqDat)

SimRVSequences documentation built on July 1, 2020, 6:03 p.m.