API for vcfR
Manipulate and Visualize VCF Data
| Global functions | |
|---|---|
| %>% | Man page |
| .CM_to_NM | Source code |
| .NM2winNM | Source code |
| .elementNumber | Source code |
| .extract_GT_to_CM | Source code |
| .extract_haps | Source code |
| .grepa | Source code |
| .gt_to_popsum | Source code |
| .onAttach | Source code |
| .rank_variants | Source code |
| .read_body_gz | Source code |
| .read_meta_gz | Source code |
| .seq_to_rects | Source code |
| .shankaR | Source code |
| .vcf_stats_gz | Source code |
| .window_init | Source code |
| .windowize_NM | Source code |
| .windowize_annotations | Source code |
| .windowize_fasta | Source code |
| .windowize_variants | Source code |
| .write_fasta | Source code |
| .write_vcf_body | Source code |
| AD_frequency | Man page 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 |
| Population genetics summaries | Man page |
| Process chromR objects | Man page |
| Ranking | Man page |
| VCF input and output | Man page |
| Windowing | Man page |
| [,vcfR,ANY,ANY,ANY-method | Man page |
| [,vcfR-method | 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 |
| check_keys | Man page Source code |
| chrom | Man page |
| chromR functions | Man page |
| chromR,chromR-method | Man page |
| chromR-class | Man page |
| chromR2vcfR | Man page Source code |
| chromR_example | Man page |
| 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_tidy | Man page Source code |
| extract_info_tidy | Man page Source code |
| freq_peak | Man page Source code |
| freq_peak_plot | 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 |
| gt.m2sfs | Source code |
| gt.to.popsum | Man page Source code |
| gt2popsum | Man page 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.indel | 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 |
| ordisample | Man page Source code |
| pair_sort | Source code |
| pairwise_genetic_diff | Man page |
| peak_to_ploid | Man page Source code |
| 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 |
| rbind2,vcfR,ANY-method | Man page |
| rbind2,vcfR,missing-method | Man page |
| rbind2,vcfR,vcfR-method | Man page |
| rbind2.vcfR | Man page |
| rePOS | Man page Source code |
| read.vcfR | Man page Source code |
| regex.win | Man page Source code |
| seq2chromR | Man page Source code |
| seq2rects | Man page 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 |
| vcfR2hapmap | Man page Source code |
| vcfR2loci | Man page Source code |
| vcfR2migrate | 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_test | Man page |
| vep | Man page |
| win.table | Man page Source code |
| windowize.NM | Man page 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 |
| z.score | Man page Source code |
