vcfR-package	vcfR
%>%	pipe
addID	addID
AD_frequency	AD_frequency
alleles2consensus	genotype_matrix
ann2chromR	create_chromR
chromo	chromo_plot
chromoqc	chromo_plot
chromo_plot	chromo_plot
chromR functions	chromR_functions
chromR,chromR-method	chromR-method
chromR-class	chromR-class
chromR2vcfR	chrom_to_vcfR
Convert to tidy data frames	vcfR_to_tidy_conversion
create.chromR	create_chromR
dim,vcfR-method	vcfR-method
dim.vcfR	vcfR-method
dna	vcfR_example
dr.plot	drplot
dr.plot elements	drplot
extract.gt	extract_gt
extract.haps	extract_gt
extract.indels	extract_gt
extract.info	extract_gt
extract_gt_tidy	vcfR_to_tidy_conversion
extract_info_tidy	vcfR_to_tidy_conversion
Format conversion	vcfR_conversion
freq_peak	freq_peak
genetic_diff	genetic_diff
Genotype matrix functions	genotype_matrix
get.alleles	genotype_matrix
getALT	getFIX
getALT,chromR-method	getFIX
getALT,vcfR-method	getFIX
getCHROM	getFIX
getCHROM,chromR-method	getFIX
getCHROM,vcfR-method	getFIX
getFILTER	getFIX
getFILTER,chromR-method	getFIX
getFILTER,vcfR-method	getFIX
getFIX	getFIX
getFIX,chromR-method	getFIX
getFIX,vcfR-method	getFIX
getID	getFIX
getID,chromR-method	getFIX
getID,vcfR-method	getFIX
getINFO	getFIX
getINFO,chromR-method	getFIX
getINFO,vcfR-method	getFIX
getPOS	getFIX
getPOS,chromR-method	getFIX
getPOS,vcfR-method	getFIX
getQUAL	getFIX
getQUAL,chromR-method	getFIX
getQUAL,vcfR-method	getFIX
getREF	getFIX
getREF,chromR-method	getFIX
getREF,vcfR-method	getFIX
gff	vcfR_example
gt.to.popsum	proc_chromR
gt2popsum	proc_chromR
head	vcfR-method
head,chromR-method	chromR-method
head,vcfR-method	vcfR-method
heatmap.bp	heatmap_bp
INFO2df	INFO2df
is.biallelic	query_gt
is.het	is_het
is.polymorphic	query_gt
is_biallelic	query_gt
is_het	is_het
length,chromR-method	chromR-method
maf	maf
masker	chromR_functions
masplit	masplit
metaINFO2df	INFO2df
names<-,chromR,character-method	chromR-method
NM2winNM	windowing
nrow,vcfR-method	vcfR-method
nrow.vcfR	vcfR-method
null.plot	drplot
ordisample	ordisample
plot	chromR-method
plot,chromR-method	chromR-method
plot,vcfR-method	vcfR-method
print,chromR-method	chromR-method
proc.chromR	proc_chromR
Process chromR objects	proc_chromR
query.gt	query_gt
queryMETA	queryMETA
rank.variants.chromR	ranking
Ranking	ranking
rbind2,vcfR,ANY-method	vcfR-method
rbind2,vcfR,missing-method	vcfR-method
rbind2,vcfR,vcfR-method	vcfR-method
rbind2.vcfR	vcfR-method
read.vcfR	io_vcfR
regex.win	proc_chromR
seq2chromR	create_chromR
seq2rects	proc_chromR
show,chromR-method	chromR-method
show,vcfR-method	vcfR-method
var.win	proc_chromR
variant.table	chromR_functions
vcf	vcfR_example
VCF input and output	io_vcfR
vcf2chromR	create_chromR
vcfR	vcfR
vcfR-class	vcfR-class
vcfR2chromR	create_chromR
vcfR2DNAbin	vcfR2DNAbin
vcfR2genind	vcfR_conversion
vcfR2genlight	vcfR_conversion
vcfR2loci	vcfR_conversion
vcfR2tidy	vcfR_to_tidy_conversion
vcfR_example	vcfR_example
vcfR_test	vcfR_test
vcf_field_names	vcfR_to_tidy_conversion
vcf_test	vcfR_test
win.table	chromR_functions
Windowing	windowing
windowize.NM	windowing
write.fasta	fasta_output
write.var.info	summary_tables
write.vcf	io_vcfR
write.win.info	summary_tables
z.score	windowing
[,vcfR,ANY,ANY,ANY-method	vcfR-method
