vcfR v1.8.0

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Functions in vcfR

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