qtlhot: Inference for QTL Hotspots
Version 0.9.0

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
URL http://www.stat.wisc.edu/~yandell/statgen
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("qtlhot")

Popular man pages

filter.threshold: Summary of threshold results
GetCandReg: Get genetic information on candidate regulators and...
GetCommonQtls: Get common QTLs for phenotypes
hotsize: Hotspot size routines.
parallel.qtlhot: Code for parallelizing R/qtlhot.
SimCrossCausal: Simulate Cross for Causal Tests
sim.hotspot: Wrapper routine for simulations.
See all...

All man pages Function index File listing

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

Functions

CMSTCross Man page
CMSTtests Man page Source code
CMSTtestsList Man page Source code
CausalRocCurve Source code
CitTests Man page Source code
CombineTests Source code
CreateTraitsLodInt Source code
DropMissing Source code
FDRplot Source code
FitAllTests Man page Source code
GetCandReg Man page Source code
GetCis Source code
GetCisCandReg Man page Source code
GetCoMappingTraits Man page Source code
GetCommonQtls Man page Source code
GetPowerFDR Source code
GetPowerFdrMatrices Source code
GetPvalsDistr Source code
GetRocMatrix Source code
GetSubsetForPlot Source code
JoinTestOutputs Man page Source code
MyMultipleTestingSim Source code
MyMultipleTestingSim2 Source code
N.WW.counts Source code
NL.counts Source code
PerformanceSummariesKo Source code Source code
PrecTpFpMatrix Man page Source code
SimCross1 Source code
SimCross2 Source code
SimCross3 Source code
SimCross4 Source code
SimCross5 Source code
SimCross6 Source code
SimCrossCausal Man page Source code
SimCrossIndep Man page Source code
add.phenos Man page Source code
add.rug Source code
big.phase0 Man page Source code
big.phase1 Source code
big.phase2 Source code
big.phase3 Source code
cat.scanone Source code
causal.ROC.curve Source code
count.thr Source code
counts Source code
do.big.phase2 Source code
exceed.thr Source code
filter.threshold Man page Source code
findpeaks Source code
get.Roc.Matrix Source code
get.chr.pos Source code
get.hotravel Source code
get.hotscan Source code
get.hotsize Source code
get.hotspot Source code
get.power.type1.prec.matrix Source code
get.power.type1.prec.matrix.2 Source code
get.tails Source code
highlod Man page Source code
highlod.thr Source code
hotperm Man page Source code
hotperm1 Man page
hotsize Man page Source code
hotsize.highlod Man page Source code
hotsize.scanone Man page Source code
include.hotspots Man page Source code
lininterp Source code
make.maxlod Source code
max.highlod Man page Source code
max.hotsize Source code
mySimulations Man page Source code Source code
myapprox Source code
mycat Source code
neqtl Source code
normal.trans Source code
p.adjust.np Man page Source code
parallel.error Source code
parallel.message Source code
parallel.qtlhot Man page Source code
performance.summaries.cit Source code
performance.summaries.cmst Source code
plot.bic.aic Source code
plot.cit Source code
plot.highlod Man page Source code
plot.hotperm Source code
plot.hotsize Man page Source code
plot.non.par.cmst Source code
plot.par.cmst Source code
plot.par.cmst.joint Source code
print.highlod Man page Source code
print.hotperm Man page Source code
print.hotsize Man page Source code
print.summary.hotperm Man page Source code
print.ww.perm Man page Source code
pull.highlod Man page Source code
pull.max Source code
qm.approx Source code
qtlhot.phase0 Man page Source code
qtlhot.phase1 Source code
qtlhot.phase2 Source code
qtlhot.phase3 Source code
quantile.highlod Man page Source code
quantile.hotperm Man page Source code
ravel.filter Source code
ravel.scan Source code
runningmean Source code
scanone.permutations Source code
sexbatch.covar Source code
sim.hotspot Man page Source code
sim.null.cross Man page Source code
sim.null.pheno.data Man page Source code
sliding.bar.plot Source code
slidingbar.create Source code
slidingbar.plot Source code
smooth.neqtl Source code
smoothall Source code
smoothchr Source code
summary.highlod Man page Source code
summary.hotperm Man page Source code
summary.hotsize Man page Source code
summary.ww.perm Man page Source code
ww.perm Man page Source code
ww.perm.highlod Source code
ww.perm.maxlod Source code

Files

inst
inst/parallel
inst/parallel/Phase1.R
inst/parallel/cross.RData
inst/parallel/params.txt
inst/parallel/Phase3.R
inst/parallel/ReadMe
inst/parallel/runparallel.sh
inst/parallel/SOAR.post.R
inst/parallel/Phase2.R
inst/parallel/Phase0.R
inst/parallel/SOAR.phase0.R
inst/notes
inst/notes/plot.R
inst/notes/cmst.txt
inst/notes/code.txt
inst/notes/perm.txt
inst/notes/vignette.txt
inst/deprecated.R
inst/doc
inst/doc/cmst.pdf
inst/doc/qtlhot.pdf
inst/doc/qtlhot.Rnw
inst/doc/cmst.R
inst/doc/qtlhot.R
inst/doc/cmst.Rnw
src
src/Makevars
src/runningmean.c
src/runningmean.h
NAMESPACE
data
data/CMSTCross.RData
data/hotperm1.RData
R
R/sliding.R
R/parallel.R
R/multiple_testing_sim_functions.R
R/big.R
R/plotcmst.R
R/simcmst.R
R/westwu.R
R/rug.R
R/add.phenos.R
R/runningmean.R
R/highlod.R
R/cmst.R
R/utilhot.R
R/study.R
R/utilcmst.R
R/simhot.R
R/ravel.R
R/roc.R
R/hotperm.R
R/max.R
R/neqtl.R
R/hotsize.R
vignettes
vignettes/savedperms.RData
vignettes/qtlhot.Rnw
vignettes/cmst.Rnw
MD5
README
build
build/vignette.rds
DESCRIPTION
man
man/hotsize.Rd
man/GetCommonQtls.Rd
man/westwu.Rd
man/GetCandReg.Rd
man/parallel.qtlhot.Rd
man/add.phenos.Rd
man/SimCrossCausal.Rd
man/hotperm.Rd
man/filter.threshold.Rd
man/sim.hotspot.Rd
man/PrecTpFpMatrix.Rd
man/CMSTtests.Rd
man/highlod.Rd
qtlhot documentation built on May 19, 2017, 10:58 a.m.

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