condSegProbF {GESE}

Computes conditional segregation probability for the family

Description

Computes the conditional probability that a variant is segregating in the family conditional on that the variant is present in one of the founders in the family.

Usage

condSegProbF(pedTemp, subjInfo)

Arguments

pedTemp

The data frame that includes the complete pedigree structure for the family

subjInfo

A data frame that contains the subject phenotype information for the sequenced subjects. it should include the columns FID, IID, and PHENOTYPE.

Value

returns the conditional segregating probability of a variant in the family

Author(s)

Dandi Qiao

References

Qiao, D. Lange, C., Laird, N.M., Won, S., Hersh, C.P., et al. (2017). Gene-based segregation method for identifying rare variants for family-based sequencing studies. Genet Epidemiol 41(4):309-319. DOI:10.1002/gepi.22037.

See Also

GESE

Examples

data(pednew)
data(mapInfo)
data(dataRaw)
data(database)
library(kinship2)
pedigrees = kinship2::pedigree(pednew$IID, pednew$faID, pednew$moID,pednew$sex,famid=pednew$FID)
subjects= dataRaw[,c(1,2,6)]
condSegProbF(pedigrees['93'], subjects)
condSegProbF(pedigrees['412'], subjects)
results2 <- GESE(pednew, database, 1000000, dataRaw, mapInfo, threshold=1e-2)
results2$condSegProb