genosegF2: Function for segmentation
In liu3zhenlab/genomap: An R Package for manipulation of genetic data

Description Usage Arguments Value Author(s) See Also Examples

F2 segmentation using genotyping data Input data requirment: genotyping data with columns of chr; pos; >=1 lines The package DNAcopy is required.

genosegF2(geno, genocols, chromosomes, chrname = "chr", posname = "pos", 
    output.common = "seg", data.type = "logratio", allele1.name = "A", 
    allele2.name = "B", hetero.name = "H", missing.name = c("0"), allele1.code = -1, 
    allele2.code = 1, hetero.code = 0, min.seg.size = 1e+05, cna.alpha = 0.01, 
    cna.nperm = 10000, cna.p.method = "perm", cna.eta = 0.01, cna.min.width = 5, 
    seg.mean.cutoffs = c(-0.8, -0.2, 0.2, 0.8))

`geno`	genotyping data, containing at least chr; pos; genotyping scores of lines
`genocols`	column numbers of individuals
`chromosomes`	chromosomes or contigs of interest for segmentation
`chrname`	column name/num of chromosomes or contigs
`posname`	column name/num of marker positions
`output.common`	the prefix name of output file
`data.type`	binary or logratio, default logratio
`missing.name`	code for missing data, could be a vector
`min.seg.size`	minimal size of segments, segments with smaller length will be ignored
`seg.mean.cutoffs`	a numeric vector with two values in between 0 and 1, c(smaller, hetero.smaller, hetero.larger, larger), segment mean values <= smaller: allele 1 segment mean values >= larger: allele 2 segment mean values in between (hetero.smaller, hetero.larger): hetero
`alleleX.name`	allele labels in the output
`alleleX.code`	allele codes as values for segmentation
`cna.xxx`	are DNAcopy parameters, please refer DNAcopy mannual