filter_vcf: Filter VCF

In geneHapR: Gene Haplotype Statistics, Phenotype Association and Visualization

Filter VCF

Description

filter VCF by GFF annotation or by position or both

Usage

filter_vcf(vcf, gff = gff,
           mode = c("POS", "type", "both"),
           Chr = Chr, start = start, end = end,
           type = c("CDS", "exon", "gene", "genome", "custom"),
           cusTyp = c("CDS", "five_prime_UTR", "three_prime_UTR"),
           geneID = geneID)

Arguments

vcf	object of vcfR class, VCF file imported by import_vcf()
gff	object of GRanges class, genome annotations imported by import_gff()
mode	filter mode, one of "POS", "type", "both"
Chr	chromosome name, needed if mode set to "POS" or "both"
start	start position, needed if mode set to "POS" or "both"
end	end position, needed if mode set to "POS" or "both"
type	filter type, needed if mode set to "type" or "both", one of "CDS", "exon", "gene", "genome", "custom", if type was set to "custom", then custom_type is needed.
cusTyp	character vector, custom filter type, needed if type set to "custom"
geneID	gene ID

Value

vcfR

Examples

# filtet vcf
data("geneHapR_test")
vcf_f1 <- filter_vcf(vcf, mode = "POS",
                    Chr = "scaffold_1",
                    start = 4300, end = 5890)

vcf_f2 <- filter_vcf(vcf, mode = "type",
                    gff = gff,
                    type = "CDS")
vcf_f3 <- filter_vcf(vcf, mode = "both",
                    Chr = "scaffold_1",
                    start = 4300, end = 5890,
                    gff = gff,
                    type = "CDS")

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