GESE (version 2.0.0)

trim_unrelated: Trims the pedigree structure to exclude multiple founder cases

Description

Trims the families to include only one founder case in each pedigree. It also exclude families with only one control subject.

Usage

trim_unrelated(seqSub, pednew2)

Arguments

seqSub

A data frame that includes at least three columns: the Family ID (FID), Individual ID (IID), and affection status (PHENOTYPE). This input values should be output from the trim_oneLineage function.

pednew2

A data frame includes the complete pedigree structure information for all sequenced families in the dataset. The required column names of this data frame include: FID (family ID), IID (individual ID, must be of class character), faID (father ID, NA if unavailable), moID (mother ID, NA if unavailable), and sex.

Value

The modified dataPed2 file after the trimming.

Details

For each pedigree,each there are multiple case founders in the pedigree, to satisfy the assumption that the causal rare variant must be introduced by one founder only, we need to keep only one case fonder that is related to most of the sequened subjects in the pedigree. We also want to remove families with no case.

References

Qiao, D. Lange, C., Laird, N.M., Won, S., Hobbs, B., et al. 2016. Gene-based segregation method for identifying rare variants for family-based sequencing studies.

See Also

GESE, trim_oneLineage

Examples

data(pednew)
data(mapInfo)
data(dataRaw)
data(database)
subjects <- dataRaw[,c(1:2, 6)]
cat("Trimming the families...\n")
cat("Trimming step 1: keep only one lineage \n")
trim <- trim_oneLineage(seqSub=subjects, pednew)
subjects2 <- trim_unrelated(trim$seqSubjUpdate, trim$pedInfoUpdate)