condSegProbF function

Computes conditional segregation probability for the family

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.

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.

Returns

returns the conditional segregating probability of a variant in the family

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.

Author(s)

Dandi Qiao

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