trim_unrelated: Trims the pedigree structure to exclude multiple founder...

In GESE: Gene-Based Segregation Test

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.

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.

Value

The modified dataPed2 file after the trimming.

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, 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)

	

Example output

Loading required package: kinship2
Loading required package: Matrix
Loading required package: quadprog
Trimming the families...
Trimming step 1: keep only one lineage 
Family  267 
Family  145 
Family  763 
Family  686 
Family  828 
Family  612 
Family  93 
Family  34 
Family  606 
Family  252 
Family  96 
Family  960 
Family  414 
Family  566 
Family  228 
Family  986 
Family  554 
Family  660 
Family  16 
Family  849 
Family  101 
Family  150 
Family  336 
Family  889 
Family  398 
Family  230 
Family  711 
Family  401 
Family  210 
Family  664 
Family  684 
Family  393 
Family  867 
Family  332 
Family  99 
Family  658 
Family  137 
Family  571 
Family  87 
Family  477 
Family  570 
Family  412 
Family  557 
Family  266 
Family  845 
Family  534 
Family  746 
Family  236 
Family  216 
Family  33 
Family  267 
--do not need to trim
Family  145 
--do not need to trim
Family  763 
--do not need to trim
Family  686 
--do not need to trim
Family  828 
--do not need to trim
Family  612 
--do not need to trim
Family  93 
--do not need to trim
Family  34 
--do not need to trim
Family  606 
--do not need to trim
Family  252 
--do not need to trim
Family  96 
--do not need to trim
Family  960 
--do not need to trim
Family  414 
--do not need to trim
Family  566 
--do not need to trim
Family  228 
--do not need to trim
Family  986 
--do not need to trim
Family  554 
--do not need to trim
Family  660 
--do not need to trim
Family  16 
--do not need to trim
Family  849 
--do not need to trim
Family  101 
--do not need to trim
Family  150 
--do not need to trim
Family  336 
--do not need to trim
Family  889 
--do not need to trim
Family  398 
--do not need to trim
Family  230 
--do not need to trim
Family  711 
--do not need to trim
Family  401 
--do not need to trim
Family  210 
--do not need to trim
Family  664 
--do not need to trim
Family  684 
--do not need to trim
Family  393 
--do not need to trim
Family  867 
--do not need to trim
Family  332 
--do not need to trim
Family  99 
--do not need to trim
Family  658 
--do not need to trim
Family  137 
Family  571 
--do not need to trim
Family  87 
--do not need to trim
Family  477 
--do not need to trim
Family  570 
--do not need to trim
Family  412 
--do not need to trim
Family  557 
--do not need to trim
Family  266 
--do not need to trim
Family  845 
--do not need to trim
Family  534 
--do not need to trim
Family  746 
--do not need to trim
Family  236 
--do not need to trim
Family  216 
--do not need to trim
Family  33 
--do not need to trim
Removed families with no case subjects:  

GESE documentation built on May 2, 2019, 3:59 a.m.