Package: vcfR 1.15.0
Brian J. Knaus
vcfR: Manipulate and Visualize VCF Data
Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file (*.vcf.gz). It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.
Authors:
vcfR_1.15.0.tar.gz
vcfR_1.15.0.tar.gz(r-4.5-noble)vcfR_1.15.0.tar.gz(r-4.4-noble)
vcfR_1.15.0.tgz(r-4.4-emscripten)vcfR_1.15.0.tgz(r-4.3-emscripten)
vcfR.pdf |vcfR.html✨
vcfR/json (API)
| # Install 'vcfR' in R: |
| install.packages('vcfR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/knausb/vcfr/issues
Last updated 11 months agofrom:3a30e2c886. Checks:OK: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 03 2024 |
| R-4.5-linux-x86_64 | OK | Oct 03 2024 |
Exports:%>%AD_frequencyaddIDalleles2consensusann2chromRcheck_keyschromochromoqcchromR2vcfRcreate.chromRdr.plotextract_gt_tidyextract_info_tidyextract.gtextract.hapsextract.indelsextract.infofreq_peakfreq_peak_plotgenetic_diffget.allelesgetALTgetCHROMgetFILTERgetFIXgetIDgetINFOgetPOSgetQUALgetREFgt.to.popsumgt2popsumheadheatmap.bpINFO2dfis_hetis.biallelicis.hetis.indelis.polymorphicmafmaskermasplitmetaINFO2dfNM2winNMnrownull.plotordisamplepairwise_genetic_diffpeak_to_ploidplotprintproc.chromRqueryMETArank.variants.chromRrbind2read.vcfRregex.winrePOSseq2chromRseq2rectsvar.winvariant.tablevcf_field_namesvcfR2chromRvcfR2DNAbinvcfR2genindvcfR2genlightvcfR2hapmapvcfR2locivcfR2migratevcfR2tidywin.tablewindowize.NMwrite.fastawrite.var.infowrite.vcfwrite.win.infoz.score
Dependencies:apecliclusterdigestdplyrfansigenericsgluelatticelifecyclemagrittrMASSMatrixmemusemgcvnlmepermutepillarpinfsc50pkgconfigR6Rcpprlangstringistringrtibbletidyselectutf8vctrsveganviridisLitewithr
Converting vcfR objects to other forms
Rendered fromconverting_data.Rmdusingknitr::rmarkdownon Oct 03 2024.Last update: 2020-01-10
Started: 2016-02-22
Introduction to vcfR
Rendered fromintro_to_vcfR.Rmdusingknitr::rmarkdownon Oct 03 2024.Last update: 2020-09-01
Started: 2016-02-22
VCF data
Rendered fromvcf_data.Rmdusingknitr::rmarkdownon Oct 03 2024.Last update: 2023-02-10
Started: 2016-02-22
vcfR workflow
Rendered fromworkflow.Rmdusingknitr::rmarkdownon Oct 03 2024.Last update: 2020-01-10
Started: 2017-01-07
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| AD_frequency | AD_frequency |
| Populate the ID column of VCF data | addID |
| Check that INFO and FORMAT keys are unique | check_keys |
| Plot chromR object | chromo chromoqc chromo_plot |
| chromR_functions | chromR functions masker variant.table win.table |
| Example chromR object. | chrom chromR_example |
| chromR class | chromR-class |
| Convert chrom objects to vcfR objects | chromR2vcfR |
| Convert vcfR objects to tidy data frames | Convert to tidy data frames extract_gt_tidy extract_info_tidy vcfR2tidy vcf_field_names |
| Create chromR object | ann2chromR create.chromR seq2chromR vcf2chromR vcfR2chromR |
| dr.plot elements | dr.plot dr.plot elements null.plot |
| Extract elements from vcfR objects | extract.gt extract.haps extract.indels extract.info is.indel |
| Convert vcfR objects to other formats | Format conversion vcfR2genind vcfR2genlight vcfR2loci |
| freq_peak | freq_peak |
| Plot freq_peak object | freq_peak_plot |
| Genetic differentiation | genetic_diff |
| Genotype matrix functions | alleles2consensus Genotype matrix functions get.alleles |
| Get elements from the fixed region of a VCF file | getALT getALT,chromR-method getALT,vcfR-method getCHROM getCHROM,chromR-method getCHROM,vcfR-method getFILTER getFILTER,chromR-method getFILTER,vcfR-method getFIX getFIX,chromR-method getFIX,vcfR-method getID getID,chromR-method getID,vcfR-method getINFO getINFO,chromR-method getINFO,vcfR-method getPOS getPOS,chromR-method getPOS,vcfR-method getQUAL getQUAL,chromR-method getQUAL,vcfR-method getREF getREF,chromR-method getREF,vcfR-method |
| Population genetics summaries | gt.to.popsum gt2popsum Population genetics summaries |
| Heatmap with barplots | heatmap.bp |
| Reformat INFO data as a data.frame | INFO2df metaINFO2df |
| Query genotypes for heterozygotes | is.het is_het |
| Minor allele frequency | maf |
| masplit | masplit |
| Ordinate a sample's data | ordisample |
| Pairwise genetic differentiation across populations | pairwise_genetic_diff |
| Convert allele balance peaks to ploidy | peak_to_ploid |
| Process chromR object | proc.chromR Process chromR objects regex.win seq2rects var.win |
| Query the gt slot | is.biallelic is.polymorphic is_biallelic query.gt |
| Query the META section of VCF data | queryMETA |
| Ranking variants within windows | rank.variants.chromR Ranking |
| Create non-overlapping positions (POS) for VCF data | rePOS |
| chromR-method | chromR,chromR-method head,chromR-method length,chromR-method names<-,chromR,character-method plot,chromR-method print,chromR-method show,chromR-method |
| show | dim,vcfR-method dim.vcfR head head,vcfR-method nrow,vcfR-method nrow.vcfR plot,vcfR-method rbind2,vcfR,ANY-method rbind2,vcfR,missing-method rbind2,vcfR,vcfR-method rbind2.vcfR show,vcfR-method [,vcfR,ANY,ANY,ANY-method [,vcfR-method |
| Read and write vcf format files | read.vcfR VCF input and output write.vcf |
| Example data for vcfR. | dna gff vcf vcfR_example |
| Test data for vcfR. | vcfR_test vcf_test |
| vcfR class | vcfR-class |
| Convert vcfR to DNAbin | vcfR2DNAbin |
| Convert a vcfR object to hapmap | vcfR2hapmap |
| Convert a vcfR object to MigrateN input file | vcfR2migrate |
| Example data from the Variant Effect Predictor (VEP). | vep |
| Create window summaries of data | NM2winNM Windowing windowize.NM z.score |
| Create fasta format output | write.fasta |
| Write summary tables from chromR objects | write.var.info write.win.info |
