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.
The data frame that includes the complete pedigree structure for the family
A data frame that contains the subject phenotype information for the sequenced subjects. it should include the columns FID, IID, and PHENOTYPE.
returns the conditional segregating probability of a variant in the family
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.
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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
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