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

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Files in this package

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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