Files in meyer-lab-cshl/plinkQC
Genotype Quality Control with 'PLINK'
.Rbuildignore
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.travis.yml
CODE_OF_CONDUCT.md
DESCRIPTION
INDEX.Rmd
INDEX.md
LICENSE
NAMESPACE
NEWS.md
R/applyQC.R
R/individualQC.R
R/markerQC.R
R/plinkQC.R
R/utils.R
README.Rmd
README.md
codemeta.json
doc/AncestryCheck.R
doc/AncestryCheck.Rmd
doc/AncestryCheck.pdf
doc/Genomes1000.R
doc/Genomes1000.Rmd
doc/Genomes1000.md
doc/Genomes1000.pdf
doc/HapMap.R
doc/HapMap.Rmd
doc/HapMap.md
doc/HapMap.pdf
doc/plinkQC.R
doc/plinkQC.Rmd
doc/plinkQC.pdf
doc/plos-genetics.csl
docs/404.html
docs/CODE_OF_CONDUCT.html
docs/LICENSE-text.html
docs/articles/AncestryCheck.html
docs/articles/AncestryCheck_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/AncestryCheck_files/anchor-sections-1.0/anchor-sections.css
docs/articles/AncestryCheck_files/anchor-sections-1.0/anchor-sections.js
docs/articles/Genomes1000.html
docs/articles/Genomes1000_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/Genomes1000_files/anchor-sections-1.0/anchor-sections.css
docs/articles/Genomes1000_files/anchor-sections-1.0/anchor-sections.js
docs/articles/HapMap.html
docs/articles/HapMap_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/HapMap_files/anchor-sections-1.0/anchor-sections.css
docs/articles/HapMap_files/anchor-sections-1.0/anchor-sections.js
docs/articles/checkAncestry.png
docs/articles/checkHetImiss.png
docs/articles/checkRelatedness.png
docs/articles/checkSex.png
docs/articles/hwe.png
docs/articles/index.html
docs/articles/individualQC.png
docs/articles/maf.png
docs/articles/markerQC.png
docs/articles/overviewAncestryQC.png
docs/articles/overviewMarkerQC.png
docs/articles/overviewQC.png
docs/articles/plinkQC.html
docs/articles/plinkQC_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/plinkQC_files/anchor-sections-1.0/anchor-sections.css
docs/articles/plinkQC_files/anchor-sections-1.0/anchor-sections.js
docs/articles/snpmissingness.png
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/extra.css
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/qc.png
docs/reference/Rplot001.png
docs/reference/checkFiltering.html
docs/reference/checkPlink.html
docs/reference/checkRemoveIDs.html
docs/reference/check_ancestry.html
docs/reference/check_het_and_miss.html
docs/reference/check_hwe.html
docs/reference/check_maf.html
docs/reference/check_relatedness.html
docs/reference/check_sex.html
docs/reference/check_snp_missingness.html
docs/reference/cleanData.html
docs/reference/evaluate_check_ancestry.html
docs/reference/evaluate_check_het_and_miss.html
docs/reference/evaluate_check_relatedness.html
docs/reference/evaluate_check_sex.html
docs/reference/index.html
docs/reference/overviewPerIndividualQC.html
docs/reference/overviewPerMarkerQC.html
docs/reference/perIndividualQC.html
docs/reference/perMarkerQC.html
docs/reference/plinkQC.html
docs/reference/relatednessFilter.html
docs/reference/run_check_ancestry.html
docs/reference/run_check_heterozygosity.html
docs/reference/run_check_missingness.html
docs/reference/run_check_relatedness.html
docs/reference/run_check_sex.html
docs/reference/testNumerics.html
inst/extdata/Genomes1000_ID2Pop.txt
inst/extdata/Genomes1000_PopColors.txt
inst/extdata/Genomes1000_sample_info.txt
inst/extdata/HapMapIII_sample_info.txt
inst/extdata/HapMap_ID2Pop.txt
inst/extdata/HapMap_PopColors.txt
inst/extdata/data.HapMapIII.eigenvec
inst/extdata/data.HapMapIII.fam
inst/extdata/data.bed
inst/extdata/data.bim
inst/extdata/data.clean.bed
inst/extdata/data.clean.bim
inst/extdata/data.clean.fam
inst/extdata/data.fam
inst/extdata/data.het
inst/extdata/data.hh
inst/extdata/data.imiss
inst/extdata/data.lmiss
inst/extdata/data.prune.in
inst/extdata/data.prune.out
inst/extdata/data.sexcheck
inst/extdata/exclude_markers
inst/extdata/extract_markers
inst/extdata/high-LD-regions-hg18-NCBI36-tolift.txt
inst/extdata/high-LD-regions-hg18-NCBI36.txt
inst/extdata/high-LD-regions-hg19-GRCh37.bed
inst/extdata/high-LD-regions-hg19-GRCh37.txt
inst/extdata/high-LD-regions-hg38-GRCh38.bed
inst/extdata/high-LD-regions-hg38-GRCh38.txt
inst/extdata/keep_individuals
inst/extdata/liftOver.cmd
inst/extdata/remove_individuals
man/checkFiltering.Rd
man/checkPlink.Rd
man/checkRemoveIDs.Rd
man/check_ancestry.Rd
man/check_het_and_miss.Rd
man/check_hwe.Rd
man/check_maf.Rd
man/check_relatedness.Rd
man/check_sex.Rd
man/check_snp_missingness.Rd
man/cleanData.Rd
man/evaluate_check_ancestry.Rd
man/evaluate_check_het_and_miss.Rd
man/evaluate_check_relatedness.Rd
man/evaluate_check_sex.Rd
man/overviewPerIndividualQC.Rd
man/overviewPerMarkerQC.Rd
man/perIndividualQC.Rd
man/perMarkerQC.Rd
man/plinkQC.Rd
man/relatednessFilter.Rd
man/run_check_ancestry.Rd
man/run_check_heterozygosity.Rd
man/run_check_missingness.Rd
man/run_check_relatedness.Rd
man/run_check_sex.Rd
man/testNumerics.Rd
pkgdown/extra.css
tests/testthat.R
tests/testthat/HapMap_ID2Pop.txt
tests/testthat/HapMap_PopColors.txt
tests/testthat/data.HapMapIII.eigenvec
tests/testthat/data.HapMapIII.eigenvec_numeric.fam
tests/testthat/data.HapMapIII_no_samples.eigenvec
tests/testthat/data.HapMapIII_some_samples.eigenvec
tests/testthat/data.bed
tests/testthat/data.bim
tests/testthat/data.clean.HapMapIII.eigenvec
tests/testthat/data.clean.bed
tests/testthat/data.clean.bim
tests/testthat/data.clean.fail-IBD.IDs
tests/testthat/data.clean.fail-het.IDs
tests/testthat/data.clean.fail-imiss.IDs
tests/testthat/data.clean.fail-sexcheck.IDs
tests/testthat/data.clean.fail.IDs
tests/testthat/data.clean.fam
tests/testthat/data.clean.frq
tests/testthat/data.clean.genome
tests/testthat/data.clean.het
tests/testthat/data.clean.hwe
tests/testthat/data.clean.imiss
tests/testthat/data.clean.lmiss
tests/testthat/data.clean.prune.in
tests/testthat/data.clean.prune.out
tests/testthat/data.clean.remove.IDs
tests/testthat/data.clean.sexcheck
tests/testthat/data.fail-IBD.IDs
tests/testthat/data.fail-ancestry.IDs
tests/testthat/data.fail-het.IDs
tests/testthat/data.fail-imiss.IDs
tests/testthat/data.fail-sexcheck.IDs
tests/testthat/data.fail.IDs
tests/testthat/data.fam
tests/testthat/data.genome
tests/testthat/data.het
tests/testthat/data.hh
tests/testthat/data.imiss
tests/testthat/data.remove.IDs
tests/testthat/data.sexcheck
tests/testthat/data_all_passing.het
tests/testthat/data_all_passing.imiss
tests/testthat/data_all_passing.sexcheck
tests/testthat/data_numeric.HapMapIII.eigenvec
tests/testthat/data_numeric.fam
tests/testthat/test-applyQC.R
tests/testthat/test-individualQC.R
tests/testthat/test-markerQC.R
tests/testthat/test-utils.R
vignettes/AncestryCheck.Rmd
vignettes/Genomes1000.Rmd
vignettes/HapMap.Rmd
vignettes/checkAncestry.png
vignettes/checkHetImiss.png
vignettes/checkRelatedness.png
vignettes/checkSex.png
vignettes/hwe.png
vignettes/individualQC.png
vignettes/maf.png
vignettes/markerQC.png
vignettes/overviewAncestryQC.png
vignettes/overviewMarkerQC.png
vignettes/overviewQC.png
vignettes/pdf/checkAncestry.pdf
vignettes/pdf/checkHetImiss.pdf
vignettes/pdf/checkRelatedness.pdf
vignettes/pdf/checkSex.pdf
vignettes/pdf/hwe.pdf
vignettes/pdf/individualQC.pdf
vignettes/pdf/maf.pdf
vignettes/pdf/markerQC.pdf
vignettes/pdf/overviewAncestryQC.pdf
vignettes/pdf/overviewMarkerQC.pdf
vignettes/pdf/overviewQC.pdf
vignettes/pdf/snpmissingness.pdf
vignettes/plinkQC.Rmd
vignettes/plos-genetics.csl
vignettes/references.bib
vignettes/snpmissingness.png
