vcfR: Manipulate and Visualize VCF Data
Version 1.5.0

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 publication2017-05-18 04:17:39 UTC
MaintainerBrian J. Knaus <briank.lists@gmail.com>
LicenseGPL
Version1.5.0
URL https://github.com/knausb/vcfR https://knausb.github.io/ vcfR_documentation/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("vcfR")

Getting started

README.md
Converting vcfR objects to other forms
Filtering data
Introduction to vcfR
Ranking data
Sequence coverage
VCF data
vcfR workflow
Visualizing VCF data 1
Visualizing VCF data 2

Popular man pages

create_chromR: Create chromR object
heatmap_bp: Heatmap with barplots
io_vcfR: Read and write vcf format files
maf: Minor allele frequency
vcfR: Variant call format files processed with vcfR.
vcfR_conversion: Convert vcfR objects to other formats
vcfR_to_tidy_conversion: Convert vcfR objects to tidy data frames
See all...

All man pages Function index File listing

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
genetic_diff: Genetic differentiation
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: show
vcfR_test: Test data for vcfR.
vcfR_to_tidy_conversion: Convert vcfR objects to tidy data frames
windowing: Create window summaries of data

Functions

Files

inst
inst/CITATION
inst/doc
inst/doc/converting_data.Rmd
inst/doc/intro_to_vcfR.html
inst/doc/visualization_1.R
inst/doc/filtering_data.R
inst/doc/vcf_data.html
inst/doc/visualization_1.Rmd
inst/doc/converting_data.R
inst/doc/visualization_2.html
inst/doc/ranking_data.Rmd
inst/doc/workflow.html
inst/doc/intro_to_vcfR.Rmd
inst/doc/sequence_coverage.html
inst/doc/filtering_data.html
inst/doc/ranking_data.html
inst/doc/sequence_coverage.Rmd
inst/doc/visualization_2.Rmd
inst/doc/visualization_2.R
inst/doc/converting_data.html
inst/doc/workflow.Rmd
inst/doc/ranking_data.R
inst/doc/vcf_data.Rmd
inst/doc/sequence_coverage.R
inst/doc/intro_to_vcfR.R
inst/doc/visualization_1.html
inst/doc/vcf_data.R
inst/doc/filtering_data.Rmd
tests
tests/testthat.R
tests/testthat
tests/testthat/test_drplot.R
tests/testthat/test_get.R
tests/testthat/test_1_vcf.R
tests/testthat/test_is_het.R
tests/testthat/test_proc_chromR.R
tests/testthat/test_vcfRtidy.R
tests/testthat/test_freq_peak.R
tests/testthat/test_chromoqc.R
tests/testthat/test_addID.R
tests/testthat/test_conversion.R
tests/testthat/test_4_vcfR2DNAbin.R
tests/testthat/test_vcfR_methods.R
tests/testthat/test_io.R
tests/testthat/test_heatmapbp.R
tests/testthat/test_genotype_matrix_functions.R
tests/testthat/test_chromR_method.R
tests/testthat/test_3_extract_gt.R
tests/testthat/test_chromo_plot.R
tests/testthat/test_10_write_vcf.R
tests/testthat/test_var_window.R
tests/testthat/test_maf.R
tests/testthat/test_genetic_diff.R
tests/testthat/test_ad_frequency.R
tests/testthat/test_rank_variants.R
tests/testthat/test_2_chromR.R
src
src/NM2winNM.cpp
src/Makevars
src/is_het.cpp
src/vcfRCommon.h
src/gt_to_popsum.cpp
src/extractGT2NM.cpp
src/ad_frequency.cpp
src/rank_variants.cpp
src/pair_sort.cpp
src/var_window.cpp
src/vcfRCommon.cpp
src/masplit.cpp
src/Makevars.win
src/init.c
src/RcppExports.cpp
src/seq_to_rects.cpp
src/vcf_io.cpp
src/freq_peak.cpp
NAMESPACE
data
data/vcfR_example.rdata
data/vcfR_test.RData
R
R/chromR-method.R
R/query_gt.R
R/vcfR-method.R
R/addID.R
R/sandbox.R
R/extract_gt.R
R/ordisample.R
R/vcfR_to_tidy_functions.R
R/AllClass.R
R/get_methods.R
R/chromo_plot.R
R/fasta_output.R
R/is_het.R
R/onUnload.R
R/heatmap_bp.R
R/vcfR_conversion.R
R/windowing.R
R/chromR_functions.R
R/RcppExports.R
R/ranking.R
R/queryMETA.R
R/proc_chromR.R
R/summary_tables.R
R/genetic_diff.R
R/genotype_matrix_functions.R
R/vcfR_example.R
R/vcfR_test.R
R/vcfR2DNAbin.R
R/io_vcfR.R
R/maf.R
R/drplot.R
R/chromR_to_vcfR.R
R/create_chromR.R
R/zzz.R
R/vcfR.R
R/INFO2df.R
vignettes
vignettes/converting_data.Rmd
vignettes/visualization_1.Rmd
vignettes/vcfR_flowchart.png
vignettes/ranking_data.Rmd
vignettes/intro_to_vcfR.Rmd
vignettes/sequence_coverage.Rmd
vignettes/visualization_2.Rmd
vignettes/workflow.Rmd
vignettes/vcfR_flowchart.dia
vignettes/vcf_data.Rmd
vignettes/filtering_data.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/vcfR2DNAbin.Rd
man/heatmap_bp.Rd
man/pipe.Rd
man/windowing.Rd
man/vcfR_conversion.Rd
man/AD_frequency.Rd
man/genotype_matrix.Rd
man/freq_peak.Rd
man/extract_gt.Rd
man/getFIX.Rd
man/vcfR_test.Rd
man/drplot.Rd
man/maf.Rd
man/addID.Rd
man/is_het.Rd
man/vcfR-method.Rd
man/fasta_output.Rd
man/INFO2df.Rd
man/chromR-class.Rd
man/ranking.Rd
man/chromo_plot.Rd
man/chromR_functions.Rd
man/queryMETA.Rd
man/create_chromR.Rd
man/query_gt.Rd
man/ordisample.Rd
man/vcfR.Rd
man/proc_chromR.Rd
man/masplit.Rd
man/chromR-method.Rd
man/io_vcfR.Rd
man/genetic_diff.Rd
man/summary_tables.Rd
man/chrom_to_vcfR.Rd
man/vcfR-class.Rd
man/vcfR_example.Rd
man/vcfR_to_tidy_conversion.Rd
cleanup
tools
tools/pinfsc50.png
vcfR documentation built on May 20, 2017, 3:24 a.m.

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