filter_hap: Filter hap

In geneHapR: Gene Haplotype Statistics, Phenotype Association and Visualization

Filter hap

Description

filter hapResult or hapSummary by remove positions or accessions or haplotypes

Usage

filter_hap(hap,
           rm.mode = c("position", "accession", "haplotype", "freq"),
           position.rm = position.rm,
           accession.rm = accession.rm,
           haplotype.rm = haplotype.rm,
           freq.min = 5)

Arguments

hap	object of hapSummary or hapResult class
rm.mode	filter mode, one of "position", "accession", "haplotype"
position.rm	numeric vector contains positions need to be removed
accession.rm	character vector contains accessions need to be removed, only hapResult can be filtered by accessions
haplotype.rm	character vector contains haplotypes need to be removed
freq.min	numeric, hapltypes with accessions number less than freq.min will be removed

Value

hapSummary or hapResult depend input

Examples

data("geneHapR_test")
hap <- filter_hap(hapResult,
                  rm.mode = c("position", "accession", "haplotype", "freq"),
                  position.rm = c(4879, 4950),
                  accession.rm = c("C1", "C9"),
                  haplotype.rm = c("H009", "H008"),
                  freq.min = 5)

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