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.

AuthorBrian J. Knaus [cre, aut], Niklaus J. Grunwald [aut], Eric C. Anderson [ctb], David J. Winter [ctb], Zhian N. Kamvar [ctb]
Date of publication2017-01-07 17:45:08
MaintainerBrian J. Knaus <briank.lists@gmail.com>
LicenseGPL
Version1.4.0

View on CRAN

Functions

\%>\% Man page
addID Man page
AD_frequency Man page
alleles2consensus Man page
ann2chromR Man page
chromo Man page
chromo_plot Man page
chromoqc Man page
chromR2vcfR Man page
chromR-class Man page
chromR functions Man page
chromR-method Man page
Convert to tidy data frames Man page
create.chromR Man page
dim.vcfR Man page
dim,vcfR-method Man page
dna Man page
dr.plot Man page
dr.plot elements Man page
extract.gt Man page
extract_gt_tidy Man page
extract.haps Man page
extract.indels Man page
extract.info Man page
extract_info_tidy Man page
Format conversion Man page
freq_peak Man page
Genotype matrix functions Man page
get.alleles Man page
getALT Man page
getALT,chromR-method Man page
getALT,vcfR-method Man page
getCHROM Man page
getCHROM,chromR-method Man page
getCHROM,vcfR-method Man page
getFILTER Man page
getFILTER,chromR-method Man page
getFILTER,vcfR-method Man page
getFIX Man page
getFIX,chromR-method Man page
getFIX,vcfR-method Man page
getID Man page
getID,chromR-method Man page
getID,vcfR-method Man page
getINFO Man page
getINFO,chromR-method Man page
getINFO,vcfR-method Man page
getPOS Man page
getPOS,chromR-method Man page
getPOS,vcfR-method Man page
getQUAL Man page
getQUAL,chromR-method Man page
getQUAL,vcfR-method Man page
getREF Man page
getREF,chromR-method Man page
getREF,vcfR-method Man page
gff Man page
gt2popsum Man page
gt.to.popsum Man page
head,chromR-method Man page
head,vcfR-method Man page
heatmap.bp Man page
INFO2df Man page
is_biallelic Man page
is.biallelic Man page
is_het Man page
is.het Man page
is.polymorphic Man page
maf Man page
masker Man page
masplit Man page
metaINFO2df Man page
names<-,chromR,character-method Man page
NM2winNM Man page
nrow.vcfR Man page
nrow,vcfR-method Man page
null.plot Man page
ordisample Man page
plot,chromR-method Man page
plot.vcfR Man page
plot,vcfR-method Man page
print,chromR-method Man page
proc.chromR Man page
Process chromR objects Man page
query.gt Man page
queryMETA Man page
Ranking Man page
rank.variants.chromR Man page
rbind2.vcfR Man page
rbind2,vcfR,ANY-method Man page
rbind2,vcfR,missing-method Man page
rbind2,vcfR,vcfR-method Man page
read.vcfR Man page
regex.win Man page
seq2chromR Man page
seq2rects Man page
show,chromR-method Man page
show,vcfR-method Man page
variant.table Man page
var.win Man page
vcf Man page
vcf2chromR Man page
vcf_field_names Man page
VCF input and output Man page
vcfR Man page
vcfR2chromR Man page
vcfR2DNAbin Man page
vcfR2genind Man page
vcfR2genlight Man page
vcfR2loci Man page
vcfR2tidy Man page
[,vcfR,ANY,ANY,ANY-method Man page
vcfR-class Man page
vcfR_example Man page
vcfR-method Man page
vcfR-package Man page
vcfR_test Man page
vcf_test Man page
Windowing Man page
windowize.NM Man page
win.table Man page
write.fasta Man page
write.var.info Man page
write.vcf Man page
write.win.info Man page
z.score Man page

Files

vcfR
vcfR/inst
vcfR/inst/CITATION
vcfR/inst/doc
vcfR/inst/doc/converting_data.Rmd
vcfR/inst/doc/intro_to_vcfR.html
vcfR/inst/doc/visualization_1.R
vcfR/inst/doc/filtering_data.R
vcfR/inst/doc/vcf_data.html
vcfR/inst/doc/visualization_1.Rmd
vcfR/inst/doc/converting_data.R
vcfR/inst/doc/visualization_2.html
vcfR/inst/doc/ranking_data.Rmd
vcfR/inst/doc/workflow.html
vcfR/inst/doc/intro_to_vcfR.Rmd
vcfR/inst/doc/sequence_coverage.html
vcfR/inst/doc/filtering_data.html
vcfR/inst/doc/ranking_data.html
vcfR/inst/doc/sequence_coverage.Rmd
vcfR/inst/doc/visualization_2.Rmd
vcfR/inst/doc/visualization_2.R
vcfR/inst/doc/converting_data.html
vcfR/inst/doc/workflow.Rmd
vcfR/inst/doc/ranking_data.R
vcfR/inst/doc/vcf_data.Rmd
vcfR/inst/doc/sequence_coverage.R
vcfR/inst/doc/intro_to_vcfR.R
vcfR/inst/doc/visualization_1.html
vcfR/inst/doc/vcf_data.R
vcfR/inst/doc/filtering_data.Rmd
vcfR/tests
vcfR/tests/testthat.R
vcfR/tests/testthat
vcfR/tests/testthat/test_drplot.R
vcfR/tests/testthat/test_get.R
vcfR/tests/testthat/test_1_vcf.R
vcfR/tests/testthat/test_is_het.R
vcfR/tests/testthat/test_vcfRtidy.R
vcfR/tests/testthat/test_freq_peak.R
vcfR/tests/testthat/test_chromoqc.R
vcfR/tests/testthat/test_addID.R
vcfR/tests/testthat/test_conversion.R
vcfR/tests/testthat/test_windowing.R
vcfR/tests/testthat/test_4_vcfR2DNAbin.R
vcfR/tests/testthat/test_vcfR_methods.R
vcfR/tests/testthat/test_io.R
vcfR/tests/testthat/test_heatmapbp.R
vcfR/tests/testthat/test_genotype_matrix_functions.R
vcfR/tests/testthat/test_chromR_method.R
vcfR/tests/testthat/test_3_extract_gt.R
vcfR/tests/testthat/test_chromo_plot.R
vcfR/tests/testthat/test_10_write_vcf.R
vcfR/tests/testthat/test_var_window.R
vcfR/tests/testthat/test_maf.R
vcfR/tests/testthat/test_ad_frequency.R
vcfR/tests/testthat/test_rank_variants.R
vcfR/tests/testthat/test_2_chromR.R
vcfR/src
vcfR/src/NM2winNM.cpp
vcfR/src/Makevars
vcfR/src/is_het.cpp
vcfR/src/vcfRCommon.h
vcfR/src/gt_to_popsum.cpp
vcfR/src/extractGT2NM.cpp
vcfR/src/ad_frequency.cpp
vcfR/src/rank_variants.cpp
vcfR/src/pair_sort.cpp
vcfR/src/var_window.cpp
vcfR/src/vcfRCommon.cpp
vcfR/src/masplit.cpp
vcfR/src/Makevars.win
vcfR/src/RcppExports.cpp
vcfR/src/seq_to_rects.cpp
vcfR/src/vcf_io.cpp
vcfR/src/freq_peak.cpp
vcfR/NAMESPACE
vcfR/data
vcfR/data/vcfR_example.rdata
vcfR/data/vcfR_test.RData
vcfR/R
vcfR/R/chromR-method.R vcfR/R/query_gt.R vcfR/R/vcfR-method.R vcfR/R/addID.R vcfR/R/sandbox.R vcfR/R/extract_gt.R vcfR/R/ordisample.R vcfR/R/vcfR_to_tidy_functions.R vcfR/R/AllClass.R vcfR/R/get_methods.R vcfR/R/chromo_plot.R vcfR/R/fasta_output.R vcfR/R/is_het.R vcfR/R/onUnload.R vcfR/R/heatmap_bp.R vcfR/R/vcfR_conversion.R vcfR/R/windowing.R vcfR/R/chromR_functions.R vcfR/R/RcppExports.R vcfR/R/ranking.R vcfR/R/queryMETA.R vcfR/R/proc_chromR.R vcfR/R/summary_tables.R vcfR/R/genotype_matrix_functions.R vcfR/R/vcfR_example.R vcfR/R/vcfR_test.R vcfR/R/vcfR2DNAbin.R vcfR/R/io_vcfR.R vcfR/R/maf.R vcfR/R/drplot.R vcfR/R/chromR_to_vcfR.R vcfR/R/create_chromR.R vcfR/R/zzz.R vcfR/R/vcfR.R vcfR/R/INFO2df.R
vcfR/vignettes
vcfR/vignettes/converting_data.Rmd
vcfR/vignettes/visualization_1.Rmd
vcfR/vignettes/vcfR_flowchart.png
vcfR/vignettes/ranking_data.Rmd
vcfR/vignettes/intro_to_vcfR.Rmd
vcfR/vignettes/sequence_coverage.Rmd
vcfR/vignettes/visualization_2.Rmd
vcfR/vignettes/workflow.Rmd
vcfR/vignettes/vcfR_flowchart.dia
vcfR/vignettes/vcf_data.Rmd
vcfR/vignettes/filtering_data.Rmd
vcfR/README.md
vcfR/MD5
vcfR/build
vcfR/build/vignette.rds
vcfR/DESCRIPTION
vcfR/man
vcfR/man/vcfR2DNAbin.Rd vcfR/man/heatmap_bp.Rd vcfR/man/pipe.Rd vcfR/man/windowing.Rd vcfR/man/vcfR_conversion.Rd vcfR/man/AD_frequency.Rd vcfR/man/genotype_matrix.Rd vcfR/man/freq_peak.Rd vcfR/man/extract_gt.Rd vcfR/man/getFIX.Rd vcfR/man/vcfR_test.Rd vcfR/man/drplot.Rd vcfR/man/maf.Rd vcfR/man/addID.Rd vcfR/man/is_het.Rd vcfR/man/vcfR-method.Rd vcfR/man/fasta_output.Rd vcfR/man/INFO2df.Rd vcfR/man/chromR-class.Rd vcfR/man/ranking.Rd vcfR/man/chromo_plot.Rd vcfR/man/chromR_functions.Rd vcfR/man/queryMETA.Rd vcfR/man/create_chromR.Rd vcfR/man/query_gt.Rd vcfR/man/ordisample.Rd vcfR/man/vcfR.Rd vcfR/man/proc_chromR.Rd vcfR/man/masplit.Rd vcfR/man/chromR-method.Rd vcfR/man/io_vcfR.Rd vcfR/man/summary_tables.Rd vcfR/man/chrom_to_vcfR.Rd vcfR/man/vcfR-class.Rd vcfR/man/vcfR_example.Rd vcfR/man/vcfR_to_tidy_conversion.Rd
vcfR/cleanup

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