Files in tobyjohnson/gtx
Genetics ToolboX

.Rbuildignore
.gitignore
DESCRIPTION
Makefile
NAMESPACE
R/PheWAS_Forestplot.R R/aba.R R/abf.R R/annot.R R/blat.R R/blockassoc.R R/cache.R R/clinical.R R/coloc.R R/demographics.R R/find_qtl_bygene.R R/finemap.R R/fitmix.R R/fixna.R R/gene.R R/glsglm.R R/grs.R R/gtx_log.R R/gtxbase.R R/gwas.R R/gwas2.R R/hapmap.R R/ideas_predict.R R/input.R R/kmplot.R R/manhattan.R R/meta.R R/mincover.R R/modules.R R/moments2.R R/mps.R R/mpssurv.R R/multimatch.R R/multipheno.R R/otplot.R R/pcaplot.R R/pgx.R R/phewas.R R/piccolo.R R/pipeline.R R/pipeline.postanalysis.R R/plantation.R R/plotutils.R R/power.R R/qq10.R R/qtplot.R R/regionplot.R R/sanitation.R R/snpdata.R R/snphwe.R R/ssm.R R/stepwise.R R/testsummary.R R/text.R R/tidy_connections.R R/transform.R R/waterfall.R R/zzz.R
data/adiponectin.scores.RData
data/agtstats.RData
data/aoex1.RData
data/bp.scores.RData
data/cad.scores.RData
data/clinex.RData
data/derivations.standard.IDSL.RData
data/derivations.standard.RData
data/gencode14.UGT1A1.RData
data/gtx.version.RData
data/height.scores.RData
data/lipid.cad.scores.RData
data/lipid.scores.RData
data/liver.scores.RData
data/magic.scores.RData
data/mthfrex.RData
data/snps.BRCA1.RData
data/t2d.scores.RData
data/t2dex.RData
gtx.Rproj
inst/python/plots.py
inst/templates/gtxpipe-report-negative.Rmd
inst/testdata/UB-138_expected.csv.gz
inst/testdata/UB-138_input.csv.gz
logs/tests.txt
man/CLEO.Rd man/Surv2.Rd man/aba.fill.Rd man/aba.flatten.Rd man/aba.int_coloc_plot.Rd man/aba.int_zoom1.Rd man/aba.int_zoom2.Rd man/aba.plot.Rd man/aba.query.Rd man/aba.save.Rd man/aba.wrapper.Rd man/aba.zoom.Rd man/abf.Wakefield.Rd man/abf.normal.Rd man/abf.t.Rd man/add_ssh_known_host.Rd man/adiponectin.scores.Rd man/agtstats.Rd man/align.snpdata.coding.Rd man/allelesAB.Rd man/annot.Rd man/aoex1.Rd man/big_copy_to.Rd man/binarise.Rd man/blockassoc.Rd man/bp.scores.Rd man/cad.scores.Rd man/chi2ncp.Rd man/clinex.Rd man/clinical.derive.Rd man/clinical.import.Rd man/close_int_conn.Rd man/coeff.extract.Rd man/coloc.Rd man/coloc.compute.Rd man/coloc.fast.Rd man/coloc_old.Rd man/combine.moments2.Rd man/config_db.Rd man/config_tmp_write_db.Rd man/contrasting.rainbow.Rd man/credset.Rd man/demographics.Rd man/derivation.add.Rd man/derivations.standard.IDSL.Rd man/derivations.standard.Rd man/drop_impala_copy.Rd man/est.moments2.Rd man/find_qtl_bygene.Rd man/finitise.Rd man/fitmix.Rd man/fitmix.plot.Rd man/fitmix.r2.Rd man/fitmix.simulate.Rd man/fixNA.Rd man/fupower.Rd man/gclambda.Rd man/gencode14.UGT1A1.Rd man/gene.Rd man/gls.approx.logistic.Rd man/grade.Rd
man/grade.Rd~
man/grs.filter.Qrs.Rd man/grs.make.scores.Rd man/grs.onesnp.apply.Rd man/grs.plot.Rd man/grs.summary.Rd man/gtx-package.Rd man/gtx.params.Rd man/gtx.version.Rd man/gtx_debug.Rd man/gtx_error.Rd man/gtx_fatal.Rd man/gtx_fatal_stop.Rd man/gtx_info.Rd man/gtx_warn.Rd man/gtxanalyses.Rd man/gtxcache.Rd man/gtxpipe.Rd man/gtxregion.Rd man/gtxversion.Rd man/gwas.Rd man/gwas2.Rd man/hapmap.read.haplotypes.Rd man/hapmap.snpdata.Rd man/height.scores.Rd man/ideas_get_states.Rd man/ideas_gwas_plot.Rd man/ideas_gwas_summarize.Rd man/ideas_lasso.Rd man/ideas_loci_summarize.Rd man/ideas_make.Rd man/ideas_predict.Rd man/ideas_preload_states.Rd man/ideas_sum_pp_cross_cell_types.Rd man/ideas_wrapper.Rd man/ile.Rd man/impala_copy_to.Rd man/int_coloc_pics_lite.Rd man/int_fastDoCall.Rd man/int_harmonize_pics.Rd man/int_sbind.Rd man/kmplot.Rd man/landmark.Rd man/lipid.cad.scores.Rd man/lipid.scores.Rd man/liver.scores.Rd man/lm.moments2.Rd man/magic.scores.Rd man/make.moments2.Rd man/manhattan.Rd man/mincover.Rd man/mlog10p.Rd man/moments2.Rd man/mps.driver.Rd man/mps.simple.Rd man/mthfrex.Rd man/multicoloc.Rd man/multicoloc2.Rd man/multimatch.Rd man/multipheno.OBrien.Rd man/multipheno.T2.Rd man/n.extract.Rd man/norm1.Rd man/otplot.Rd man/parse.snps.Rd man/pcaplot.Rd man/pgx.endpoints.Rd man/pgx.exposure.Rd man/pgx.trtreat.Rd man/phewas.Rd man/piccolo.Rd man/pics_calc.Rd man/plantation.Rd man/plotpos.by.chr.Rd man/positivise.Rd
man/positivise.Rd~
man/prettye.Rd man/prettypc.Rd man/prune.distance.Rd man/prune.genes.Rd man/qq10.Rd man/qtplot.Rd man/read.snpdata.impute.Rd man/read.snpdata.mach.Rd man/read.snpdata.minimac.Rd man/read.snpdata.plink.Rd man/regionplot.Rd man/remap.q2t.Rd man/replaceNA.Rd man/retrieve_data.Rd man/safe.Rd man/sanitise.whitespace.Rd man/snpdata.Rd man/snphwe.Rd man/snphweCounts.Rd man/snps.BRCA1.Rd man/stepdown.moments2.Rd man/stepup.moments2.Rd man/t2d.scores.Rd man/t2dex.Rd man/test.extract.Rd man/test.subsample.Rd man/text2factor.Rd
man/text2factor.Rd~
man/textgrid.Rd man/tokenise.whitespace.Rd man/trial.params.Rd man/twopq.Rd man/validate_impala.Rd man/validate_module_input.Rd man/validate_sc.Rd man/valuesof.Rd man/waterfall.Rd man/whoami.Rd man/zise.Rd tests/testthat.R tests/testthat/setup-xyz.R tests/testthat/teardown-xyz.R tests/testthat/test-QTLs.R tests/testthat/test-coloc.R tests/testthat/test-gwas.R tests/testthat/test-my-test.R tests/testthat/test-phewas.R tests/testthat/test-regionplot.R tests/testthat/test-tables_are_present.R
vignettes/ashg2012.Rnw
vignettes/demographics.Rmd
tobyjohnson/gtx documentation built on June 8, 2019, 1:32 p.m.