vcfR: Manipulate and Visualize VCF Data

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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.

Author
Brian J. Knaus [cre, aut], Niklaus J. Grunwald [aut], Eric C. Anderson [ctb], David J. Winter [ctb], Zhian N. Kamvar [ctb]
Date of publication
2016-12-08 15:30:07
Maintainer
Brian J. Knaus <briank.lists@gmail.com>
License
GPL
Version
1.3.0

View on CRAN

Man pages

addID
Populate the ID column of VCF data
AD_frequency
AD_frequency
chromo_plot
Plot chromR object
chromR-class
chromR class
chromR_functions
chromR_functions
chromR-method
chromR-method
chrom_to_vcfR
Convert chrom objects to vcfR objects
create_chromR
Create chromR object
drplot
dr.plot elements
extract_gt
Extract elements from vcfR objects
fasta_output
Create fasta format output
freq_peak
freq_peak
genotype_matrix
Genotype matrix functions
getFIX
Get elements from the fixed region of a VCF file
heatmap_bp
Heatmap with barplots
INFO2df
Reformat INFO data as a data.frame
io_vcfR
Read and write vcf format files
is_het
Query genotypes for heterozygotes
maf
Minor allele frequency
masplit
masplit
ordisample
Ordinate a sample's data
pipe
Pipe operator
proc_chromR
Process chromR object
query_gt
Query the gt slot
queryMETA
Query the META section of VCF data
ranking
Ranking variants within windows
summary_tables
Write summary tables from chromR objects
vcfR
Variant call format files processed with vcfR.
vcfR2DNAbin
Convert vcfR to DNAbin
vcfR-class
vcfR class
vcfR_conversion
Convert vcfR objects to other formats
vcfR_example
Example data for vcfR.
vcfR-method
vcfR-method
vcfR_test
Test data for vcfR.
vcfR_to_tidy_conversion
Convert vcfR objects to tidy data frames
windowing
Create window summaries of data

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/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/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/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