Manipulate and Visualize VCF Data

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Documentation for package ‘vcfR’ version 1.15.0

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A C D E F G H I L M N O P Q R S V W Z misc

-- A --

addID Populate the ID column of VCF data
AD_frequency AD_frequency
alleles2consensus Genotype matrix functions
ann2chromR Create chromR object

-- C --

check_keys Check that INFO and FORMAT keys are unique
chrom Example chromR object.
chromo Plot chromR object
chromoqc Plot chromR object
chromo_plot Plot chromR object
chromR functions chromR_functions
chromR-class chromR class
chromR-method chromR-method
chromR2vcfR Convert chrom objects to vcfR objects
chromR_example Example chromR object.
Convert to tidy data frames Convert vcfR objects to tidy data frames
create.chromR Create chromR object

-- D --

dim-method show
dim.vcfR show
dna Example data for vcfR.
dr.plot dr.plot elements
dr.plot elements dr.plot elements

-- E --

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
extract_gt_tidy Convert vcfR objects to tidy data frames
extract_info_tidy Convert vcfR objects to tidy data frames

-- F --

Format conversion Convert vcfR objects to other formats
freq_peak freq_peak
freq_peak_plot Plot freq_peak object

-- G --

genetic_diff Genetic differentiation
Genotype matrix functions Genotype matrix functions
get.alleles Genotype matrix functions
getALT Get elements from the fixed region of a VCF file
getALT-method Get elements from the fixed region of a VCF file
getCHROM Get elements from the fixed region of a VCF file
getCHROM-method Get elements from the fixed region of a VCF file
getFILTER Get elements from the fixed region of a VCF file
getFILTER-method Get elements from the fixed region of a VCF file
getFIX Get elements from the fixed region of a VCF file
getFIX-method Get elements from the fixed region of a VCF file
getID Get elements from the fixed region of a VCF file
getID-method Get elements from the fixed region of a VCF file
getINFO Get elements from the fixed region of a VCF file
getINFO-method Get elements from the fixed region of a VCF file
getPOS Get elements from the fixed region of a VCF file
getPOS-method Get elements from the fixed region of a VCF file
getQUAL Get elements from the fixed region of a VCF file
getQUAL-method Get elements from the fixed region of a VCF file
getREF Get elements from the fixed region of a VCF file
getREF-method Get elements from the fixed region of a VCF file
gff Example data for vcfR.
gt.to.popsum Population genetics summaries
gt2popsum Population genetics summaries

-- H --

head show
head-method chromR-method
head-method show
heatmap.bp Heatmap with barplots

-- I --

INFO2df Reformat INFO data as a data.frame
is.biallelic Query the gt slot
is.het Query genotypes for heterozygotes
is.indel Extract elements from vcfR objects
is.polymorphic Query the gt slot
is_biallelic Query the gt slot
is_het Query genotypes for heterozygotes

-- L --

length-method chromR-method

-- M --

maf Minor allele frequency
masker chromR_functions
masplit masplit
metaINFO2df Reformat INFO data as a data.frame

-- N --

names<--method chromR-method
NM2winNM Create window summaries of data
nrow-method show
nrow.vcfR show
null.plot dr.plot elements

-- O --

ordisample Ordinate a sample's data

-- P --

pairwise_genetic_diff Pairwise genetic differentiation across populations
peak_to_ploid Convert allele balance peaks to ploidy
plot-method chromR-method
plot-method show
Population genetics summaries Population genetics summaries
print-method chromR-method
proc.chromR Process chromR object
Process chromR objects Process chromR object

-- Q --

query.gt Query the gt slot
queryMETA Query the META section of VCF data

-- R --

rank.variants.chromR Ranking variants within windows
Ranking Ranking variants within windows
rbind2-method show
rbind2.vcfR show
read.vcfR Read and write vcf format files
regex.win Process chromR object
rePOS Create non-overlapping positions (POS) for VCF data

-- S --

seq2chromR Create chromR object
seq2rects Process chromR object
show-method chromR-method
show-method show

-- V --

var.win Process chromR object
variant.table chromR_functions
vcf Example data for vcfR.
VCF input and output Read and write vcf format files
vcf2chromR Create chromR object
vcfR-class vcfR class
vcfR2chromR Create chromR object
vcfR2DNAbin Convert vcfR to DNAbin
vcfR2genind Convert vcfR objects to other formats
vcfR2genlight Convert vcfR objects to other formats
vcfR2hapmap Convert a vcfR object to hapmap
vcfR2loci Convert vcfR objects to other formats
vcfR2migrate Convert a vcfR object to MigrateN input file
vcfR2tidy Convert vcfR objects to tidy data frames
vcfR_example Example data for vcfR.
vcfR_test Test data for vcfR.
vcf_field_names Convert vcfR objects to tidy data frames
vcf_test Test data for vcfR.
vep Example data from the Variant Effect Predictor (VEP).

-- W --

win.table chromR_functions
Windowing Create window summaries of data
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 --

z.score Create window summaries of data

-- misc --

[-method show