get.brks: Picking chromosomal breaking points

In bbms09/TrioSim: Simulating Triad Genomewide Genotypes

Description

The breaking points at each chromosome can be picked manually or use this function. When a data frame containing the recombination rates (rcmb.rate) is provided the function tends to pick the breaking points at recombination hotspots.

Usage

get.brks(N.brk, n.ped, snp.all2, target.snp, rcmb.rate = NA,
  same.brk = FALSE)

Arguments

N.brk	is an integer giving the number of breaks to be picked for each chromosome.
n.ped	is an integer giving the number of trios to be simulated
snp.all2	is a dataframe containing the list of SNPs in PLINK .bim format. Two columns of the dataframe is used: column 1 with column name "V1" containing the chromosome number and column 4 with column name "V4" containing the chromosomal postion of the SNPs.
target.snp	is a vector of integers showing the row number of the target SNPs in the .bim file.
rcmb.rate	the default value is NA. rcmb.rate is a dataframe containing the recombination rates at each SNP. The ordering of the SNPs should be identical to that of snp.all2. It contains 4 columns with column names 'CHR','RS','POS',and 'RATE with the corresponding values for "the chromosomal number", "SNP rs number", "chromosomal position", and "recombination rate". The recombination rate represents the maximum recombination rate in the chromosomal region between the current SNP and the SNP above (or the first basepair of the chromosome for the first SNP on a chromosome). When no rcmb.rate is provided the function will pick the breaking points randomly where keeping the breaking points in between target SNPs. An example recombination rate data frame "rcmb.rate" is already loaded with the package.
same.brk	is an indicator variable to denote whethere the same set of breaking points will be used for all simulated triads

Value

A list of two elements is returned. The first one is a matrix of integers showing where the chromosomal breaks is to take place for each individuals in the simulated trios. The second one is a matrix showing the chromosomal segments out of which each target SNP is selected for each simulated trio.

Examples

tar.snp <- c(21, 118, 121, 140, 155, 168, 218, 383) 
found.brks <- get.brks(N.brk=3,n.ped=1000, snp.all2, tar.snp,rcmb.rate=NA)
breaks <- found.brks[[1]]
family.pos <- found.brks[[2]] 

bbms09/TrioSim documentation built on May 11, 2019, 9:27 p.m.