testR/genosegF2.example.R

In liu3zhenlab/genomap: An R Package for manipulation of genetic data

setwd("~/RProjects/genoseg/testR/")
source("genosegF2.R")
source("seg2scores.R")

### load data
d <- read.delim("../raw/genodata.txt")

### generate segments
segres <- genosegF2(geno = d, genocols = c(5,6), chrname = "CHR", posname = "POS",
                    output.common = "test", chromosomes = c(1, 10),
                    allele1.name = "A", allele2.name = "B", hetero.name = "H", missing.name = 0)

### genotyping scoring
seg2score(seg.input = "test.seg.txt", segscore.output = "test.segmarker.txt", missing.data.code = 0, binsize = 1000000)