gRec: Variant filtering with recessive inheritance considering...
In BartBroeckx/Mendelian: Variant Analysis for Mendelian Disorders

Description Usage Arguments Details Author(s) Examples

gRec should be used to filter variants under a recessive mode of inheritance when common functional units (a gene, an exon, ...) should be considered.

1	gRec(x, y, list)

`x`	the case(s).
`y`	optional, the control(s).
`list`	logical, specify whether a list should be returned (TRUE) or not (false).

gRec checks for common functional units within cases. For a unit to be retained, it should have at least one homozygous non-reference variant or at least be compound heterozygous. If variants from control(s) are present, they can be used to filter variants from the cases. Homozygous variants present in the controls will be used to filter variants from the cases immediately. Pairwise combinations of heterozygous variants present in the controls can also be used to filter variants in the cases. In addition, various detectance and penetrance parameters can be specified during the processing.

Before using this function, each file from each case should have been processed by CLCfile or VCFfile with annot.

The parameter list allows you to specify whether the output should contain only the retained variants and genes (FALSE) only or together with the compound heterozygous variants per sample (TRUE). This parameter is only useful when you have both case(s) and control(s) and when compound heterozygous variants were present in the controls. For further processing with commonvar, list should be FALSE.

Bart Broeckx

CLCfile1proc <-CLCfile(CLCfile1, "Coding.region.change", TRUE, "; ")
CLCfile2proc <-CLCfile(CLCfile2, "Coding.region.change", TRUE, "; ")
output <- gRec("CLCfile1proc", "CLCfile2proc", TRUE)
output
output <- gRec(c("CLCfile1proc","CLCfile2proc"),, TRUE)
output