gen.simuHaplo_traceback {GENLIB}

Trace inheritance path for results from gene dropping simulation

Description

Given the output of a gene dropping simulation using gen.simuHaplo, this function can trace the inheritance path of a proband segment back to the founder it is inherited from

Usage

gen.simuHaplo_traceback(gen, proID, ancestorID, all_nodes_path, proband_haplotypes_path)

Arguments

gen

An object of class GLgen obtained with gen.genealogy, gen.lineages or gen.branching. Required.

proID

Integer ID of the proband to trace back from.

ancestorID

Integer ID of the founder, any segment in the proband haplotype inherited from this founder will be traced back

all_nodes_path

String of the path to the "All_nodes_haplotypes.txt" output file generated by gen.simulHaplo

proband_haplotypes_path

String of the path to the "Proband_Haplotypes.txt" output file generated by gen.simulHaplo

Value

returns a dataframe with the following columns: "simulNo", "seg_length", "path_no". For every simulation in the output files where the specified proband inherits a segment from the specified founder. "seg_length" is the length of the inherited segment in BP. "path_no" is an integer that specifies the path of inheritance of the segment Unique paths of inheritance are simply identified by the order they appear in the outputs file, and the full paths (ID of every individual along the path) are printed to the R console. If this is not appearing check that messages are not disabled.

See Also

gen.genealogy gen.simuHaplo gen.simuHaplo_IBD_compare

Examples

gen_table <- data.frame(ind=c(1,2,3,4,5,6,7),
                        mother=c(0,0,2,0,0,5,3),
                        father=c(0,0,1,0,0,4,6),
                        sex=c(1,2,2,1,2,1,1)
)

#convert the genealogy table into a GENLIB object
sample_gen<-gen.genealogy(gen_table) 

gen.graph(sample_gen)
# Simulate the gene dropping from founders to probamds

gen.simuHaplo(sample_gen, simulNo=5, model = 1, model_params = c(1,1), cM_len=c(100,100),
                BP_len = 100000000, all_nodes = 1, outDir=tempdir())

traceback <-gen.simuHaplo_traceback(sample_gen, 7, 1,
                        paste(tempdir(), "All_nodes_haplotypes.txt", sep = "/"),
                        paste(tempdir(), "Proband_Haplotypes.txt", sep="/"))