vcfR-package | Variant call format files processed with vcfR. |
alleles2consensus | Genotype matrix functions |
ann2chromR | Create chromR object |
chromo | Plot chromR object |
chromoqc | Plot chromR object |
chromo_plot | Plot chromR object |
chromR functions | chromR_functions |
chromR-class | chromR class |
chromR-methods | Create chromR object |
chromR2vcfR | Convert chrom objects to vcfR objects |
create.chromR | Create chromR object |
dim-method | vcfR methods |
dim.vcfR | vcfR methods |
dna | Example data for vcfR. |
dr plot elements | dr plot elements |
dr.plot | dr plot elements |
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 |
Format conversion | Convert vcfR objects to other formats |
Genotype matrix functions | Genotype matrix functions |
get.alleles | Genotype matrix functions |
getCHROM | Create chromR object |
getFIX | Create chromR object |
getPOS | Create chromR object |
getQUAL | Create chromR object |
gff | Example data for vcfR. |
gt.to.popsum | Process chromR object |
gt2popsum | Process chromR object |
head-method | chromR methods |
head-method | vcfR methods |
head.chromR | chromR methods |
heatmap.bp | Heatmap with barplots |
is.biallelic | Query the gt slot |
is.polymorphic | Query the gt slot |
is_biallelic | Query the gt slot |
masker | chromR_functions |
names-method | chromR methods |
names.chromR | chromR methods |
NM2winNM | Create window summaries of data |
nrow-method | vcfR methods |
nrow.vcfR | vcfR methods |
null.plot | dr plot elements |
plot-method | chromR methods |
plot-method | vcfR methods |
plot.chromR | chromR methods |
plot.vcfR | vcfR methods |
proc.chromR | Process chromR object |
Process chromR objects | Process chromR object |
query.gt | Query the gt slot |
rank.variants.chromR | Ranking variants within windows |
Ranking | Ranking variants within windows |
rbind2-method | vcfR methods |
rbind2.vcfR | vcfR methods |
read.vcfR | Read and write vcf format files |
regex.win | Process chromR object |
seq2chromR | Create chromR object |
seq2rects | Process chromR object |
show-method | chromR methods |
show-method | vcfR methods |
var.win | Process chromR object |
variant.table | chromR_functions |
vcf | Example data for vcfR. |
vcf2chromR | Create chromR object |
vcfR | Variant call format files processed with vcfR. |
vcfR-class | vcfR class |
vcfR-methods | vcfR methods |
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 |
vcfR_example | Example data for vcfR. |
win.table | chromR_functions |
Windowing | Create window summaries of data |
windowize | chromR methods |
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.score | Create window summaries of data |
[-method | vcfR methods |