hap2hmp: Convert hapResult object to hapmap (hmp) format, for interact...

In geneHapR: Gene Haplotype Statistics, Phenotype Association and Visualization

Convert hapResult object to hapmap (hmp) format, for interact with other packages

Description

Convert hapResult object to hapmap (hmp) format, for interact with other packages

Usage

hap2hmp(hap)

hmp2hap(hmp, hapPrefix = "H", hetero_remove = TRUE, na_drop = TRUE, ...)

Arguments

hap	object of "hapResult" class
hmp	object of "data.frame" class in hapmap format
hapPrefix	prefix of haplotype names
hetero_remove	whether remove accessions contains hyb-sites, Character not A T C G
na_drop	whether drop accessions contains missing data ("N", "NA", ".")
...	Arguments passed on to table2hap 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" pad The number length in haplotype names should be extend to.

Value

a data.frame in hapmap format.

Examples

data("geneHapR_test")
hmp <- hap2hmp(hapResult)
hap <- hmp2hap(hmp)

geneHapR documentation built on May 29, 2024, 11:59 a.m.