Files in plinkQC
Genotype Quality Control with 'PLINK'
MD5
NEWS.md
NAMESPACE
DESCRIPTION
LICENSE
R/sysdata.rda
R/applyQC.R
R/ancestry.R
R/markerQC.R
R/individualQC.R
R/plinkQC-package.R
R/utils.R
inst/doc/plinkQC.Rmd
inst/doc/AncestryCheck.html
inst/doc/Genomes1000.Rmd
inst/doc/plinkQC.R
inst/doc/my-vignette.R
inst/doc/my-vignette.Rmd
inst/doc/AncestryCheck.R
inst/doc/plinkQC.pdf
inst/doc/HapMap.Rmd
inst/doc/HapMap.pdf
inst/doc/Genomes1000.pdf
inst/doc/HapMap.R
inst/doc/Genomes1000.R
inst/doc/my-vignette.html
inst/doc/AncestryCheck.Rmd
inst/extdata/high-LD-regions-hg19-GRCh37.bed
inst/extdata/data.hg38.bim
inst/extdata/HapMap_ID2Pop.txt
inst/extdata/keep_individuals
inst/extdata/data.hg38.bed
inst/extdata/data.bim
inst/extdata/data.bed
inst/extdata/high-LD-regions-hg38-GRCh38.bed
inst/extdata/high-LD-regions-hg18-NCBI36-tolift.txt
inst/extdata/data.clean.bed
inst/extdata/liftOver.cmd
inst/extdata/HapMap_PopColors.txt
inst/extdata/exclude_markers
inst/extdata/high-LD-regions-hg18-NCBI36.txt
inst/extdata/remove_individuals
inst/extdata/final_model.RDS
inst/extdata/high-LD-regions-hg38-GRCh38.txt
inst/extdata/data.hg38.fam
inst/extdata/data.hh
inst/extdata/high-LD-regions-hg19-GRCh37.txt
inst/extdata/extract_markers
inst/extdata/data.clean.bim
inst/extdata/data.fam
inst/extdata/Genomes1000_PopColors.txt
inst/extdata/data.clean.fam
build/vignette.rds
build/partial.rdb
tests/testthat.R
tests/testthat/data.clean.remove.IDs
tests/testthat/test-markerQC.R
tests/testthat/data.clean.fail-imiss.IDs
tests/testthat/data.hg38.renamed.pvar
tests/testthat/data.clean.fail-sexcheck.IDs
tests/testthat/HapMap_ID2Pop.txt
tests/testthat/data.clean.lmiss
tests/testthat/data.pgen
tests/testthat/data.clean.pgen
tests/testthat/data.clean.fail-IBD.IDs
tests/testthat/data.fail.IDs
tests/testthat/test-utils.R
tests/testthat/data.bim
tests/testthat/data.bed
tests/testthat/data.hg38.renamed.pgen
tests/testthat/data.sexcheck
tests/testthat/data.clean.pvar
tests/testthat/data.log
tests/testthat/test-ancestry.R
tests/testthat/data.fail-sexcheck.IDs
tests/testthat/data_all_passing.het
tests/testthat/data_numeric.HapMapIII.eigenvec
tests/testthat/data.clean.sscore
tests/testthat/data_numeric.fam
tests/testthat/data_all_passing.imiss
tests/testthat/data.clean.bed
tests/testthat/data.sscore
tests/testthat/data.clean.prune.out
tests/testthat/data.HapMapIII.eigenvec_numeric.fam
tests/testthat/HapMap_PopColors.txt
tests/testthat/data.pvar
tests/testthat/data.exclude-ancestry.IDs
tests/testthat/data.hg38.renamed.fam
tests/testthat/data.hg38.log
tests/testthat/data.fail-IBD.IDs
tests/testthat/data.HapMapIII_some_samples.eigenvec
tests/testthat/data.clean.fail-het.IDs
tests/testthat/data.clean.het
tests/testthat/data.fail-het.IDs
tests/testthat/data.clean.frq
tests/testthat/data.clean.imiss
tests/testthat/data.imiss
tests/testthat/data.remove.IDs
tests/testthat/data.het
tests/testthat/Rplots.pdf
tests/testthat/data.fail-imiss.IDs
tests/testthat/data.hg38.renamed.bed
tests/testthat/data.clean.psam
tests/testthat/data.sscore.tmp
tests/testthat/data_all_passing.sexcheck
tests/testthat/data.hg38.renamed.psam
tests/testthat/data.clean.prune.in
tests/testthat/data.hg38.renamed.bim
tests/testthat/data.genome
tests/testthat/test-individualQC.R
tests/testthat/data.clean.genome
tests/testthat/data.HapMapIII.eigenvec
tests/testthat/data.hh
tests/testthat/data.HapMapIII_no_samples.eigenvec
tests/testthat/test-applyQC.R
tests/testthat/data.hg38.sscore
tests/testthat/data.psam
tests/testthat/data.clean.log
tests/testthat/data.clean.hwe
tests/testthat/data.clean.fail.IDs
tests/testthat/data.clean.sexcheck
tests/testthat/data.clean.bim
tests/testthat/data.fam
tests/testthat/data.clean.fam
vignettes/plinkQC.Rmd
vignettes/hwe.png
vignettes/snpmissingness.png
vignettes/Genomes1000.Rmd
vignettes/overviewQC.png
vignettes/checkAncestry.png
vignettes/overviewAncestryQC.png
vignettes/plos-genetics.csl
vignettes/checkRelatedness.png
vignettes/my-vignette.Rmd
vignettes/overviewMarkerQC.png
vignettes/checkHetImiss.png
vignettes/references.bib
vignettes/ancestral_prediction.pdf
vignettes/HapMap.Rmd
vignettes/ancestral_prediction.png
vignettes/individualQC.pdf
vignettes/individualQC.png
vignettes/markerQC.png
vignettes/AncestryCheck.Rmd
vignettes/maf.png
vignettes/checkSex.png
vignettes/pdf/checkRelatedness.pdf
vignettes/pdf/hwe.pdf
vignettes/pdf/checkHetImiss.pdf
vignettes/pdf/checkSex.pdf
vignettes/pdf/checkAncestry.pdf
vignettes/pdf/overviewAncestryQC.pdf
vignettes/pdf/snpmissingness.pdf
vignettes/pdf/maf.pdf
vignettes/pdf/individualQC.pdf
vignettes/pdf/overviewMarkerQC.pdf
vignettes/pdf/markerQC.pdf
vignettes/pdf/overviewQC.pdf
man/checkPlink2.Rd
man/checkLoadingMat.Rd
man/check_relatedness.Rd
man/check_sex.Rd
man/evaluate_check_relatedness.Rd
man/run_ancestry_prediction.Rd
man/run_check_heterozygosity.Rd
man/overviewPerIndividualQC.Rd
man/check_snp_missingness.Rd
man/run_check_missingness.Rd
man/relatednessFilter.Rd
man/evaluate_check_sex.Rd
man/cleanData.Rd
man/plinkQC-package.Rd
man/check_het_and_miss.Rd
man/evaluate_check_het_and_miss.Rd
man/check_hwe.Rd
man/run_check_relatedness.Rd
man/ancestry_prediction.Rd
man/evaluate_ancestry_prediction.Rd
man/run_check_sex.Rd
man/overviewPerMarkerQC.Rd
man/testNumerics.Rd
man/perMarkerQC.Rd
man/check_maf.Rd
man/checkRemoveIDs.Rd
man/rename_variant_identifiers.Rd
man/run_ancestry_format.Rd
man/checkPlink.Rd
man/pruning_ld.Rd
man/perIndividualQC.Rd
man/checkFiltering.Rd
man/convert_to_plink2.Rd
