qtlhot: Inference for QTL Hotspots

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Functions to infer co-mapping trait hotspots and causal models

Author
Elias Chaibub Neto <echaibub@hotmail.com> and Brian S Yandell <byandell@wisc.edu>
Date of publication
2013-09-19 08:54:03
Maintainer
Brian S. Yandell <byandell@wisc.edu>
License
GPL (>= 2)
Version
0.9.0
URLs

View on CRAN

Man pages

add.phenos
Add phenotypes to cross object.
CMSTtests
Perform CMST Tests on cross object
filter.threshold
Summary of threshold results
GetCandReg
Get genetic information on candidate regulators and...
GetCommonQtls
Get common QTLs for phenotypes
highlod
Pull high LOD values with chr and pos.
hotperm
Conduct NL and N permutation tests
hotsize
Hotspot size routines.
parallel.qtlhot
Code for parallelizing R/qtlhot.
PrecTpFpMatrix
Determine false positive and true positive rates for known...
SimCrossCausal
Simulate Cross for Causal Tests
sim.hotspot
Wrapper routine for simulations.
westwu
Conduct West-Wu (Q) permutation tests

Files in this package

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