geneHapR (version 1.2.4)

table2hap: table2hap

Description

convert variants stored in table format into hapResult

Usage

table2hap(x, hapPrefix = "H", pad = 3, hetero_remove = TRUE, na_drop = TRUE)

Value

object of hapSummary class

Arguments

x

a data.frame contains variants information. The first file column are fix as Chrome name, position, reference nuclieotide, alter nuclieotide and INFO. Accession genotype should be in followed columns. "-" will be treated as Indel. "." and "N" will be treated as missing data. Heterozygotes should be "A/T", "AAA/A"

hapPrefix

prefix of haplotype names

pad

The number length in haplotype names should be extend to.

hetero_remove

whether remove accessions contains hyb-sites, Character not A T C G

na_drop

whether drop accessions contains missing data ("N", "NA", ".")

Examples

# \donttest{
   data("geneHapR_test")
   hapResult <- table2hap(gt.geno, hapPrefix = "H",
                          hetero_remove = TRUE,
                          na_drop = TRUE)
# }