API for vcfR
Manipulate and Visualize VCF Data

Global functions
AD_frequency Man page Source code
CM_to_NM Source code
Convert to tidy data frames Man page
Format conversion Man page
Genotype matrix functions Man page
INFO2df Man page Source code
NM2winNM Man page Source code Source code
Process chromR objects Man page
Ranking Man page
VCF input and output Man page
Windowing Man page
[,vcfR,ANY,ANY,ANY-method Man page
\%>\% Man page
addID Man page Source code
alleles2consensus Man page Source code
ann2chromR Man page Source code
calc_jost Source code
calc_nei Source code
chromR functions Man page
chromR,chromR-method Man page
chromR-class Man page
chromR2vcfR Man page Source code
chromo Man page Source code
chromo_plot Man page
chromoqc Man page Source code
create.chromR Man page Source code
dim,vcfR-method Man page
dim.vcfR Man page
dna Man page
dr.plot Man page Source code
dr.plot elements Man page
extract.gt Man page Source code
extract.haps Man page Source code
extract.indels Man page Source code
extract.info Man page Source code
extract_GT_to_CM Source code
extract_GT_to_CM2 Source code
extract_gt_tidy Man page Source code
extract_haps Source code
extract_info_tidy Man page Source code
freq_peak Man page Source code
genetic_diff Man page Source code
get.alleles Man page Source code
getALT Man page Source code
getALT,chromR-method Man page
getALT,vcfR-method Man page
getCHROM Man page Source code
getCHROM,chromR-method Man page
getCHROM,vcfR-method Man page
getFILTER Man page Source code
getFILTER,chromR-method Man page
getFILTER,vcfR-method Man page
getFIX Man page Source code
getFIX,chromR-method Man page
getFIX,vcfR-method Man page
getID Man page Source code
getID,chromR-method Man page
getID,vcfR-method Man page
getINFO Man page Source code
getINFO,chromR-method Man page
getINFO,vcfR-method Man page
getPOS Man page Source code
getPOS,chromR-method Man page
getPOS,vcfR-method Man page
getQUAL Man page Source code
getQUAL,chromR-method Man page
getQUAL,vcfR-method Man page
getREF Man page Source code
getREF,chromR-method Man page
getREF,vcfR-method Man page
gff Man page
grepa Source code
gt.m2sfs Source code
gt.to.popsum Man page Source code
gt2popsum Man page Source code
gt_to_popsum Source code
guess_types Source code
head Man page
head,chromR-method Man page
head,vcfR-method Man page
heatmap.bp Man page Source code
is.biallelic Man page Source code
is.het Man page Source code
is.polymorphic Man page Source code
is_biallelic Man page
is_het Man page Source code
length,chromR-method Man page
linkage Source code
maf Man page Source code
masker Man page Source code
masplit Man page Source code
metaINFO2df Man page Source code
names<-,chromR,character-method Man page
nice Source code
nrow,vcfR-method Man page
nrow.vcfR Man page
null.plot Man page Source code
onAttach Source code
onUnload Source code
ordisample Man page Source code
pair_sort Source code
plot Man page
plot,chromR-method Man page
plot,vcfR-method Man page
plot.sfs Source code
print,chromR-method Man page
proc.chromR Man page Source code
query.gt Man page
queryMETA Man page Source code
rank.variants.chromR Man page Source code
rank_variants Source code
rbind2,vcfR,ANY-method Man page
rbind2,vcfR,missing-method Man page
rbind2,vcfR,vcfR-method Man page
rbind2.vcfR Man page Man page Man page
read.vcfR Man page Source code
read_body_gz Source code
read_meta_gz Source code
regex.win Man page Source code
seq2chromR Man page Source code
seq2rects Man page Source code
seq_to_rects Source code
set.pop1 Source code
set.pop2 Source code
show,chromR-method Man page
show,vcfR-method Man page
thetas Source code
var.win Man page Source code
variant.table Man page Source code
vcf Man page
vcf2chromR Man page
vcfR Man page
vcfR-class Man page
vcfR-package Man page
vcfR2DNAbin Man page Source code
vcfR2chromR Man page Source code
vcfR2genind Man page Source code
vcfR2genlight Man page Source code
vcfR2loci Man page Source code
vcfR2tidy Man page Source code
vcfR_example Man page
vcfR_test Man page
vcf_field_names Man page Source code
vcf_stats_gz Source code
vcf_test Man page
win.table Man page Source code
window_init Source code
windowize.NM Man page Source code
windowize_NM Source code
windowize_annotations Source code
windowize_fasta Source code
windowize_variants Source code
write.fasta Man page Source code
write.var.info Man page Source code
write.vcf Man page Source code
write.win.info Man page Source code
write_fasta Source code
write_vcf_body Source code
z.score Man page Source code
vcfR documentation built on May 30, 2017, 5:36 a.m.