Tools for Working with Variant Call Format ('VCF') Files


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Documentation for package ‘vcfR’ version 1.0.0

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vcfR-package Variant call format files processed with vcfR.
alleles2consensus Genotype matrix functions
ann2chromR Create chromR object
chromo Plot chromR object
chromoqc Plot chromR object
chromo_plot Plot chromR object
chromR functions chromR_functions
chromR-class chromR class
chromR-methods Create chromR object
chromR2vcfR Convert chrom objects to vcfR objects
create.chromR Create chromR object
dim-method vcfR methods
dim.vcfR vcfR methods
dna Example data for vcfR.
dr plot elements dr plot elements
dr.plot dr plot elements
extract.gt Extract elements from vcfR objects
extract.haps Extract elements from vcfR objects
extract.indels Extract elements from vcfR objects
extract.info Extract elements from vcfR objects
Format conversion Convert vcfR objects to other formats
Genotype matrix functions Genotype matrix functions
get.alleles Genotype matrix functions
getCHROM Create chromR object
getFIX Create chromR object
getPOS Create chromR object
getQUAL Create chromR object
gff Example data for vcfR.
gt.to.popsum Process chromR object
gt2popsum Process chromR object
head-method chromR methods
head-method vcfR methods
head.chromR chromR methods
heatmap.bp Heatmap with barplots
is.biallelic Query the gt slot
is.polymorphic Query the gt slot
is_biallelic Query the gt slot
masker chromR_functions
names-method chromR methods
names.chromR chromR methods
NM2winNM Create window summaries of data
nrow-method vcfR methods
nrow.vcfR vcfR methods
null.plot dr plot elements
plot-method chromR methods
plot-method vcfR methods
plot.chromR chromR methods
plot.vcfR vcfR methods
proc.chromR Process chromR object
Process chromR objects Process chromR object
query.gt Query the gt slot
rank.variants.chromR Ranking variants within windows
Ranking Ranking variants within windows
rbind2-method vcfR methods
rbind2.vcfR vcfR methods
read.vcfR Read and write vcf format files
regex.win Process chromR object
seq2chromR Create chromR object
seq2rects Process chromR object
show-method chromR methods
show-method vcfR methods
var.win Process chromR object
variant.table chromR_functions
vcf Example data for vcfR.
vcf2chromR Create chromR object
vcfR Variant call format files processed with vcfR.
vcfR-class vcfR class
vcfR-methods vcfR methods
vcfR2chromR Create chromR object
vcfR2DNAbin Convert vcfR to DNAbin
vcfR2genind Convert vcfR objects to other formats
vcfR2genlight Convert vcfR objects to other formats
vcfR2loci Convert vcfR objects to other formats
vcfR_example Example data for vcfR.
win.table chromR_functions
Windowing Create window summaries of data
windowize chromR methods
windowize.NM Create window summaries of data
write.fasta Create fasta format output
write.var.info Write summary tables from chromR objects
write.vcf Read and write vcf format files
write.win.info Write summary tables from chromR objects
z.score Create window summaries of data
[-method vcfR methods