vcfR v1.9.0

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Functions in vcfR

Name Description
addID Populate the ID column of VCF data
create.chromR Create chromR object
getFIX Get elements from the fixed region of a VCF file
heatmap.bp Heatmap with barplots
freq_peak_plot Plot freq_peak object
freq_peak freq_peak
write.fasta Create fasta format output
pairwise_genetic_diff Pairwise genetic differentiation across populations
gt2popsum Population genetics summaries
extract.gt Extract elements from vcfR objects
ordisample Ordinate a sample's data
genetic_diff Genetic differentiation
dr.plot elements dr.plot elements
peak_to_ploid Convert allele balance peaks to ploidy
VCF input and output Read and write vcf format files
is_het Query genotypes for heterozygotes
Genotype matrix functions Genotype matrix functions
%>% Pipe operator
Convert to tidy data frames Convert vcfR objects to tidy data frames
vcfR-class vcfR class
vcfR_test Test data for vcfR.
show,vcfR-method show
write.var.info Write summary tables from chromR objects
vcfR2DNAbin Convert vcfR to DNAbin
maf Minor allele frequency
vcfR2migrate Convert a vcfR object to MigrateN input file
Ranking Ranking variants within windows
Process chromR objects Process chromR object
rePOS Create non-overlapping positions (POS) for VCF data
vcfR Variant call format files processed with vcfR.
masplit masplit
vep Example data from the Variant Effect Predictor (VEP).
queryMETA Query the META section of VCF data
Windowing Create window summaries of data
query.gt Query the gt slot
Format conversion Convert vcfR objects to other formats
vcfR_example Example data for vcfR.
check_keys Check that INFO and FORMAT keys are unique
INFO2df Reformat INFO data as a data.frame
show,chromR-method chromR-method
chromo_plot Plot chromR object
chromR-class chromR class
chromR2vcfR Convert chrom objects to vcfR objects
AD_frequency AD_frequency
chromR functions chromR_functions
chromR_example Example chromR object.
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Vignettes of vcfR

Name
converting_data.Rmd
intro_to_vcfR.Rmd
vcfR_flowchart.dia
vcfR_flowchart.png
vcf_data.Rmd
workflow.Rmd
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