vcfR (version 1.4.0)

getFIX: Get elements from the fixed region of a VCF file

Description

Both chromR objects and vcfR objects contain a region with fixed variables. These accessors allow you to isolate these variables from these objects.

Usage

getFIX(x, getINFO = FALSE)
getCHROM(x)
getPOS(x)
getQUAL(x)
getALT(x)
getREF(x)
getID(x)
getFILTER(x)
getINFO(x)

Arguments

x

a vcfR or chromR object

getINFO

logical specifying whether getFIX should return the INFO column

Value

a vector or data frame

Examples

# NOT RUN {
library("vcfR")
data("vcfR_example")
chrom <- create.chromR('sc50', seq=dna, vcf=vcf, ann=gff)
getFIX(vcf) %>% head
getFIX(chrom) %>% head

getCHROM(vcf) %>% head
getCHROM(chrom) %>% head

getPOS(vcf) %>% head
getPOS(chrom) %>% head

getID(vcf) %>% head
getID(chrom) %>% head

getREF(vcf) %>% head
getREF(chrom) %>% head

getALT(vcf) %>% head
getALT(chrom) %>% head

getQUAL(vcf) %>% head
getQUAL(chrom) %>% head

getFILTER(vcf) %>% head
getFILTER(chrom) %>% head

getINFO(vcf) %>% head
getINFO(chrom) %>% head

# }