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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

library("vcfR")
data("vcfR_example")
data("chromR_example")
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

vcfR

Manipulate and Visualize VCF Data

v1.12.0
GPL-3
Authors
Brian J. Knaus [cre, aut] (<https://orcid.org/0000-0003-1665-4343>), Niklaus J. Grunwald [aut] (<https://orcid.org/0000-0003-1656-7602>), Eric C. Anderson [ctb], David J. Winter [ctb], Zhian N. Kamvar [ctb] (<https://orcid.org/0000-0003-1458-7108>), Javier F. Tabima [ctb] (<https://orcid.org/0000-0002-3603-2691>)
Initial release

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