# Manipulate and Visualize VCF Data

## Documentation for package ‘vcfR’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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 | Variant call format files processed with vcfR.
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
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