Man pages for vcfR
Manipulate and Visualize VCF Data

addIDPopulate the ID column of VCF data
AD_frequencyAD_frequency
check_keysCheck that INFO and FORMAT keys are unique
chromo_plotPlot chromR object
chromR-classchromR class
chromR_exampleExample chromR object.
chromR_functionschromR_functions
chromR-methodchromR-method
chrom_to_vcfRConvert chrom objects to vcfR objects
create_chromRCreate chromR object
drplotdr.plot elements
extract_gtExtract elements from vcfR objects
fasta_outputCreate fasta format output
freq_peakfreq_peak
freq_peak_plotPlot freq_peak object
genetic_diffGenetic differentiation
genotype_matrixGenotype matrix functions
getFIXGet elements from the fixed region of a VCF file
heatmap_bpHeatmap with barplots
INFO2dfReformat INFO data as a data.frame
io_vcfRRead and write vcf format files
is_hetQuery genotypes for heterozygotes
mafMinor allele frequency
masplitmasplit
ordisampleOrdinate a sample's data
pairwise_genetic_diffPairwise genetic differentiation across populations
peak_to_ploidConvert allele balance peaks to ploidy
pipePipe operator
pop_gen_sumPopulation genetics summaries
proc_chromRProcess chromR object
query_gtQuery the gt slot
queryMETAQuery the META section of VCF data
rankingRanking variants within windows
rePOSCreate non-overlapping positions (POS) for VCF data
summary_tablesWrite summary tables from chromR objects
vcfRVariant call format files processed with vcfR.
vcfR2DNAbinConvert vcfR to DNAbin
vcfR2migrateConvert a vcfR object to MigrateN input file
vcfR-classvcfR class
vcfR_conversionConvert vcfR objects to other formats
vcfR_exampleExample data for vcfR.
vcfR-methodshow
vcfR_testTest data for vcfR.
vcfR_to_tidy_conversionConvert vcfR objects to tidy data frames
vepExample data from the Variant Effect Predictor (VEP).
windowingCreate window summaries of data
vcfR documentation built on April 18, 2018, 1:03 a.m.