qtlhot: Inference for QTL Hotspots

Functions to infer co-mapping trait hotspots and causal models

AuthorElias Chaibub Neto <echaibub@hotmail.com> and Brian S Yandell <byandell@wisc.edu>
Date of publication2013-09-19 08:54:03
MaintainerBrian S. Yandell <byandell@wisc.edu>
LicenseGPL (>= 2)
Version0.9.0
http://www.stat.wisc.edu/~yandell/statgen

View on CRAN

Functions

add.phenos Man page
big.phase0 Man page
CitTests Man page
CMSTCross Man page
CMSTtests Man page
CMSTtestsList Man page
filter.threshold Man page
FitAllTests Man page
GetCandReg Man page
GetCisCandReg Man page
GetCoMappingTraits Man page
GetCommonQtls Man page
highlod Man page
hotperm Man page
hotperm1 Man page
hotsize Man page
hotsize.highlod Man page
hotsize.scanone Man page
include.hotspots Man page
JoinTestOutputs Man page
max.highlod Man page
mySimulations Man page
p.adjust.np Man page
parallel.qtlhot Man page
plot.highlod Man page
plot.hotsize Man page
PrecTpFpMatrix Man page
print.highlod Man page
print.hotperm Man page
print.hotsize Man page
print.summary.hotperm Man page
print.ww.perm Man page
pull.highlod Man page
qtlhot.phase0 Man page
quantile.highlod Man page
quantile.hotperm Man page
SimCrossCausal Man page
SimCrossIndep Man page
sim.hotspot Man page
sim.null.cross Man page
sim.null.pheno.data Man page
summary.highlod Man page
summary.hotperm Man page
summary.hotsize Man page
summary.ww.perm Man page
ww.perm Man page

Files

qtlhot
qtlhot/inst
qtlhot/inst/parallel
qtlhot/inst/parallel/Phase1.R
qtlhot/inst/parallel/cross.RData
qtlhot/inst/parallel/params.txt
qtlhot/inst/parallel/Phase3.R
qtlhot/inst/parallel/ReadMe
qtlhot/inst/parallel/runparallel.sh
qtlhot/inst/parallel/SOAR.post.R
qtlhot/inst/parallel/Phase2.R
qtlhot/inst/parallel/Phase0.R
qtlhot/inst/parallel/SOAR.phase0.R
qtlhot/inst/notes
qtlhot/inst/notes/plot.R
qtlhot/inst/notes/cmst.txt
qtlhot/inst/notes/code.txt
qtlhot/inst/notes/perm.txt
qtlhot/inst/notes/vignette.txt
qtlhot/inst/deprecated.R
qtlhot/inst/doc
qtlhot/inst/doc/cmst.pdf
qtlhot/inst/doc/qtlhot.pdf
qtlhot/inst/doc/qtlhot.Rnw
qtlhot/inst/doc/cmst.R
qtlhot/inst/doc/qtlhot.R
qtlhot/inst/doc/cmst.Rnw
qtlhot/src
qtlhot/src/Makevars
qtlhot/src/runningmean.c
qtlhot/src/runningmean.h
qtlhot/NAMESPACE
qtlhot/data
qtlhot/data/CMSTCross.RData
qtlhot/data/hotperm1.RData
qtlhot/R
qtlhot/R/sliding.R qtlhot/R/parallel.R qtlhot/R/multiple_testing_sim_functions.R qtlhot/R/big.R qtlhot/R/plotcmst.R qtlhot/R/simcmst.R qtlhot/R/westwu.R qtlhot/R/rug.R qtlhot/R/add.phenos.R qtlhot/R/runningmean.R qtlhot/R/highlod.R qtlhot/R/cmst.R qtlhot/R/utilhot.R qtlhot/R/study.R qtlhot/R/utilcmst.R qtlhot/R/simhot.R qtlhot/R/ravel.R qtlhot/R/roc.R qtlhot/R/hotperm.R qtlhot/R/max.R qtlhot/R/neqtl.R qtlhot/R/hotsize.R
qtlhot/vignettes
qtlhot/vignettes/savedperms.RData
qtlhot/vignettes/qtlhot.Rnw
qtlhot/vignettes/cmst.Rnw
qtlhot/MD5
qtlhot/README
qtlhot/build
qtlhot/build/vignette.rds
qtlhot/DESCRIPTION
qtlhot/man
qtlhot/man/hotsize.Rd qtlhot/man/GetCommonQtls.Rd qtlhot/man/westwu.Rd qtlhot/man/GetCandReg.Rd qtlhot/man/parallel.qtlhot.Rd qtlhot/man/add.phenos.Rd qtlhot/man/SimCrossCausal.Rd qtlhot/man/hotperm.Rd qtlhot/man/filter.threshold.Rd qtlhot/man/sim.hotspot.Rd qtlhot/man/PrecTpFpMatrix.Rd qtlhot/man/CMSTtests.Rd qtlhot/man/highlod.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.