Files in knausb/vcfR

Manipulate and Visualize VCF Data

.Rbuildignore

.github/.gitignore

.github/workflows/R-CMD-check.yaml

.gitignore

DESCRIPTION

NAMESPACE

NEWS.md R/AllClass.R R/INFO2df.R R/RcppExports.R R/addID.R R/check_keys.R R/chromR-method.R R/chromR_example.R R/chromR_functions.R R/chromR_to_vcfR.R R/chromo_plot.R R/create_chromR.R R/drplot.R R/extract_gt.R R/fasta_output.R R/freq_peak_plot.R R/genetic_diff.R R/genotype_matrix_functions.R R/get_methods.R R/gt_to_popsum.R R/heatmap_bp.R R/io_vcfR.R R/is_het.R R/maf.R R/onUnload.R R/ordisample.R R/pairwise_genetic_diff.R R/peak_to_ploid.R R/pipe.R R/proc_chromR.R R/queryMETA.R R/query_gt.R R/ranking.R R/rePOS.R R/sandbox.R R/summary_tables.R R/vcfR-method.R R/vcfR-package.R R/vcfR.R R/vcfR2DNAbin.R R/vcfR2hapmap.R R/vcfR2migrate.R R/vcfR_conversion.R R/vcfR_example.R R/vcfR_test.R R/vcfR_to_tidy_functions.R R/vep.R R/windowing.R R/zzz.R README.md

appveyor.yml

cleanup

cran-comments.md

data/chromR_example.RData

data/vcfR_example.rdata

data/vcfR_test.RData

data/vep.RData

inst/CITATION

man/AD_frequency.Rd man/INFO2df.Rd man/addID.Rd man/check_keys.Rd man/chromR-class.Rd man/chromR-method.Rd man/chromR_example.Rd man/chromR_functions.Rd man/chrom_to_vcfR.Rd man/chromo_plot.Rd man/create_chromR.Rd man/drplot.Rd man/extract_gt.Rd man/fasta_output.Rd man/freq_peak.Rd man/freq_peak_plot.Rd man/genetic_diff.Rd man/genotype_matrix.Rd man/getFIX.Rd man/heatmap_bp.Rd man/io_vcfR.Rd man/is_het.Rd man/maf.Rd man/masplit.Rd man/ordisample.Rd man/pairwise_genetic_diff.Rd man/peak_to_ploid.Rd man/pipe.Rd man/pop_gen_sum.Rd man/proc_chromR.Rd man/queryMETA.Rd man/query_gt.Rd man/ranking.Rd man/rePOS.Rd man/summary_tables.Rd man/vcfR-class.Rd man/vcfR-method.Rd man/vcfR-package.Rd man/vcfR2DNAbin.Rd man/vcfR2hapmap.Rd man/vcfR2migrate.Rd man/vcfR_conversion.Rd man/vcfR_example.Rd man/vcfR_test.Rd man/vcfR_to_tidy_conversion.Rd man/vep.Rd man/windowing.Rd

revdep/.gitignore

revdep/README.md revdep/cran.md

revdep/email.yml

revdep/failures.md revdep/problems.md

src/.gitignore

src/Makevars

src/Makevars.win

src/NM2winNM.cpp

src/RcppExports.cpp

src/ad_frequency.cpp

src/deprecated_funcs.cpp

src/extract_gt.cpp

src/freq_peak.cpp

src/gt_to_popsum.cpp

src/is_het.cpp

src/masplit.cpp

src/pair_sort.cpp

src/rank_variants.cpp

src/read_vcfR.cpp

src/seq_to_rects.cpp

src/var_window.cpp

src/vcfRCommon.cpp

src/vcfRCommon.h

src/write_vcfR.cpp

tests/testthat.R tests/testthat/test_010_vcfR.R tests/testthat/test_011_vcfR_methods.R tests/testthat/test_012_write_vcfR_cpp.R tests/testthat/test_013_read_vcfR_cpp.R tests/testthat/test_014_read_vcfR.R tests/testthat/test_015_write_vcfR.R tests/testthat/test_020_chromR.R tests/testthat/test_INFO2df.R tests/testthat/test_ad_frequency.R tests/testthat/test_addID.R tests/testthat/test_chromR_method.R tests/testthat/test_chromo_plot.R tests/testthat/test_conversion.R tests/testthat/test_drplot.R tests/testthat/test_extract_gt.R tests/testthat/test_freq_peak.R tests/testthat/test_freq_peak_plot.R tests/testthat/test_genetic_diff.R tests/testthat/test_genotype_matrix_functions.R tests/testthat/test_get.R tests/testthat/test_heatmapbp.R tests/testthat/test_is_het.R tests/testthat/test_maf.R tests/testthat/test_peak_to_ploid.R tests/testthat/test_proc_chromR.R tests/testthat/test_queryMETA.R tests/testthat/test_query_gt.R tests/testthat/test_rank_variants.R tests/testthat/test_rePOS.R tests/testthat/test_summary_tables.R tests/testthat/test_var_window.R tests/testthat/test_vcfR2DNAbin.R tests/testthat/test_vcfR2hapmap.R tests/testthat/test_vcfR2migrate.R tests/testthat/test_vcfRtidy.R

tools/hexagon_template.svg

tools/pinfsc50.png

tools/vcfR_hexagon.svg

tools/vcfR_hexagon_v2.svg

tools/vcfR_hexagon_v3.svg

tools/vcfR_hexagon_v4.svg

vcfR.Rproj

vignettes/converting_data.Rmd vignettes/intro_to_vcfR.Rmd

vignettes/vcfR_flowchart.dia

vignettes/vcfR_flowchart.png

vignettes/vcf_data.Rmd vignettes/workflow.Rmd

knausb/vcfR documentation built on Jan. 14, 2024, 1:56 a.m.