A C D E F G H I L M N O P Q R S V W Z misc
| vcfR-package | Variant call format files processed with vcfR. |
| addID | Populate the ID column of VCF data |
| AD_frequency | AD_frequency |
| alleles2consensus | Genotype matrix functions |
| ann2chromR | Create chromR object |
| check_keys | Check that INFO and FORMAT keys are unique |
| chrom | Example chromR object. |
| chromo | Plot chromR object |
| chromoqc | Plot chromR object |
| chromo_plot | Plot chromR object |
| chromR functions | chromR_functions |
| chromR-class | chromR class |
| chromR-method | chromR-method |
| chromR2vcfR | Convert chrom objects to vcfR objects |
| chromR_example | Example chromR object. |
| Convert to tidy data frames | Convert vcfR objects to tidy data frames |
| create.chromR | Create chromR object |
| dim-method | show |
| dim.vcfR | show |
| dna | Example data for vcfR. |
| dr.plot | dr.plot elements |
| dr.plot elements | 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 |
| extract_gt_tidy | Convert vcfR objects to tidy data frames |
| extract_info_tidy | Convert vcfR objects to tidy data frames |
| Format conversion | Convert vcfR objects to other formats |
| freq_peak | freq_peak |
| freq_peak_plot | Plot freq_peak object |
| genetic_diff | Genetic differentiation |
| Genotype matrix functions | Genotype matrix functions |
| get.alleles | Genotype matrix functions |
| getALT | Get elements from the fixed region of a VCF file |
| getALT-method | Get elements from the fixed region of a VCF file |
| getCHROM | Get elements from the fixed region of a VCF file |
| getCHROM-method | Get elements from the fixed region of a VCF file |
| getFILTER | Get elements from the fixed region of a VCF file |
| getFILTER-method | Get elements from the fixed region of a VCF file |
| getFIX | Get elements from the fixed region of a VCF file |
| getFIX-method | Get elements from the fixed region of a VCF file |
| getID | Get elements from the fixed region of a VCF file |
| getID-method | Get elements from the fixed region of a VCF file |
| getINFO | Get elements from the fixed region of a VCF file |
| getINFO-method | Get elements from the fixed region of a VCF file |
| getPOS | Get elements from the fixed region of a VCF file |
| getPOS-method | Get elements from the fixed region of a VCF file |
| getQUAL | Get elements from the fixed region of a VCF file |
| getQUAL-method | Get elements from the fixed region of a VCF file |
| getREF | Get elements from the fixed region of a VCF file |
| getREF-method | Get elements from the fixed region of a VCF file |
| gff | Example data for vcfR. |
| gt.to.popsum | Population genetics summaries |
| gt2popsum | Population genetics summaries |
| head | show |
| head-method | chromR-method |
| head-method | show |
| heatmap.bp | Heatmap with barplots |
| INFO2df | Reformat INFO data as a data.frame |
| is.biallelic | Query the gt slot |
| is.het | Query genotypes for heterozygotes |
| is.polymorphic | Query the gt slot |
| is_biallelic | Query the gt slot |
| is_het | Query genotypes for heterozygotes |
| length-method | chromR-method |
| maf | Minor allele frequency |
| masker | chromR_functions |
| masplit | masplit |
| metaINFO2df | Reformat INFO data as a data.frame |
| names<--method | chromR-method |
| NM2winNM | Create window summaries of data |
| nrow-method | show |
| nrow.vcfR | show |
| null.plot | dr.plot elements |
| ordisample | Ordinate a sample's data |
| pairwise_genetic_diff | Pairwise genetic differentiation across populations |
| peak_to_ploid | Convert allele balance peaks to ploidy |
| plot | chromR-method |
| plot-method | chromR-method |
| plot-method | show |
| Population genetics summaries | Population genetics summaries |
| print-method | chromR-method |
| proc.chromR | Process chromR object |
| Process chromR objects | Process chromR object |
| query.gt | Query the gt slot |
| queryMETA | Query the META section of VCF data |
| rank.variants.chromR | Ranking variants within windows |
| Ranking | Ranking variants within windows |
| rbind2-method | show |
| rbind2.vcfR | show |
| read.vcfR | Read and write vcf format files |
| regex.win | Process chromR object |
| rePOS | Create non-overlapping positions (POS) for VCF data |
| seq2chromR | Create chromR object |
| seq2rects | Process chromR object |
| show-method | chromR-method |
| show-method | show |
| var.win | Process chromR object |
| variant.table | chromR_functions |
| vcf | Example data for vcfR. |
| VCF input and output | Read and write vcf format files |
| vcf2chromR | Create chromR object |
| vcfR | Variant call format files processed with vcfR. |
| vcfR-class | vcfR class |
| 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 |
| vcfR2migrate | Convert a vcfR object to MigrateN input file |
| vcfR2tidy | Convert vcfR objects to tidy data frames |
| vcfR_example | Example data for vcfR. |
| vcfR_test | Test data for vcfR. |
| vcf_field_names | Convert vcfR objects to tidy data frames |
| vcf_test | Test data for vcfR. |
| vep | Example data from the Variant Effect Predictor (VEP). |
| win.table | chromR_functions |
| Windowing | Create window summaries of data |
| 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 | show |