get_hap: generat haps from vcf

In ZhangRenL/quickHapR: R Packages for Gene Haplotype Analysis

generat haps from vcf

Description

generate hap format from vcf.

Usage

get_hap(vcf,
        hapPrefix = "H",
        filter_Chr = FALSE,
        Chr = "scaffold_1",
        filter_POS = FALSE,
        startPOS = 104,
        endPOS = 9889,
        hyb_remove = TRUE,
        na.drop = TRUE)

Arguments

vcf	vcf
hapPrefix	hapPrefix, defalt is "H"
filter_Chr	filter vcf by Chrome or not, defalt is FALSE. If TRUE, the Chr is needed.
Chr	Needed for filter vcf by Chrom
filter_POS	filter vcf by Position or not, defalt is FALSE. If TRUE, startPOS and endPOS are needed.
startPOS, endPOS	Needed for filter vcf by position. startPOS must less than endPOS
hyb_remove	Remove accessions contains hybrid site or not. Defalt is TRUE.
na.drop	Drop Accessions contains unknown allele site or note. Defalt is TRUE

Value

data.frame, first four rows are fixed to meta information: CHR, POS, INFO, ALLELE Hap names were placed in col1, Accessions were placed at the last col.

Author(s)

Zhangrenl

Examples

data("quickHap_test")
# You can import your vcf data by `import_vcf()` here
hap <- get_hap(vcf,hyb_remove = TRUE, na.drop =TRUE)
hapResult <- hap_result(hap)
plotHapTable(hapResult)

ZhangRenL/quickHapR documentation built on June 17, 2022, 12:04 a.m.