multic: Quantitative Linkage Analysis Tools using the Variance Components Approach

Calculate the polygenic and major gene models for quantitative trait linkage analysis using variance components approach. The 0.2.2 release includes bug fixes that allow 'multic' to run properly on 64-bit systems. The 0.3.0 release includes a fully implemented sw2mloci() function. As of 0.3.8, Splus version is no longer supported. Additional documentation and examples can be found in the inst directory.

AuthorEric Lunde, Mariza de Andrade, Beth Atkinson, Pat Votruba
Date of publication2016-01-29 11:18:30
MaintainerPat Votruba <votruba.patrick@mayo.edu>
LicenseGPL (>= 2) | file LICENSE
Version0.4.3.1

View on CRAN

Functions

addGE Man page
add.heritability Man page
all.equal.multic Man page
apply.sequential.ids Man page
calculate.coefficients Man page
calculate.correlations Man page
calculate.cor.values Man page
calculate.descriptives Man page
calculate.initial.values Man page
canonical.path.name Man page
check.data.for.missing.values Man page
check.for.full.data Man page
clean Man page
collapseMibd Man page
combine.null.and.alt.initial.values Man page
copy.files.to.tmp.space Man page
create.multic.object Man page
expand.data Man page
expand.locus Man page
expandMibd Man page
expand.mloci Man page
expand.multic Man page
expand.share Man page
fitted.multic Man page
fixibd Man page
formula.multic Man page
gene.eff Man page
get.basename Man page
get.cm.close.to.peak Man page
get.cM.from.v.mat Man page
get.covariance.indices Man page
get.df.mix Man page
get.dist Man page
get.extension Man page
get.family.count Man page
get.family.parent.inconsistancies Man page
get.family.sizes Man page
get.major.diagonal.indices Man page
get.max.lod.and.locus Man page
get.n Man page
get.p.mix Man page
get.share.order Man page
get.top.n.families Man page
get.unique.families Man page
get.var.covar.labels Man page
get.variances.from.file Man page
gunzip Man page
gzip Man page
herit.se Man page
is.multic Man page
is.parent.offspring Man page
is.sibling Man page
is.spouse Man page
lappend Man page
lm.ready.check Man page
load.effects Man page
load.family.log.likelihoods Man page
load.inv.exp.sec.der.fixed Man page
load.inv.exp.sec.der.random Man page
load.iterations Man page
load.residuals Man page
load.var.sandwich Man page
load.v.matrices Man page
load.v.matrix.file Man page
load.y.beta.diffs Man page
load.y.beta.file Man page
make.block.id.pair Man page
make.kinship.file Man page
max.multic Man page
mergeWithKinship Man page
missing.value Man page
mlociCut Man page
mloci.split Man page
multic Man page
[.multic Man page
multic.colnames Man page
multic.control Man page
multic.is.dir Man page
multic.kurtosis Man page
multic.mkdir Man page
multic.object Man page
multic.rownames Man page
multic.skewness Man page
multic.strings.split Man page
multic.strsplit Man page
multic.system Man page
multic.unlink Man page
non.user.level.objects Man page
normalize.mibd Man page
parse.trait.names Man page
pchisq.mix Man page
phi2share Man page
plot.family.lods Man page
plotFamilyLods Man page
plot.multic Man page
polygene Man page
print.multic Man page
print.summary.multic Man page
read.pedindex.out Man page
recover.multic Man page
remove.file Man page
remove.temp.files Man page
residuals.multic Man page
run.alternative.multic Man page
solar2mloci Man page
solar2multic Man page
sortIbdCols Man page
subsets Man page
summary.multic Man page
sw2mloci Man page
t.rank Man page
tRank Man page
trim Man page
upp.tri.as.vector Man page
using.R Man page
validate.parents Man page
validate.share.out Man page
write.alt.initial.values Man page
write.initial.values Man page

Files

multic
multic/inst
multic/inst/examples
multic/inst/examples/solarOutput
multic/inst/examples/solarOutput/simulated.ped
multic/inst/examples/solarOutput/phi2.gz
multic/inst/examples/solarOutput/solarMibds
multic/inst/examples/solarOutput/solarMibds/mibd.5.3.gz
multic/inst/examples/solarOutput/solarMibds/mibd.5.0.gz
multic/inst/examples/solarOutput/solarMibds/mibd.5.5.gz
multic/inst/examples/solarOutput/solarMibds/mibd.5.1.gz
multic/inst/examples/solarOutput/solarMibds/mibd.5.2.gz
multic/inst/examples/solarOutput/solarMibds/mibd.5.4.gz
multic/inst/examples/solarOutput/simulated.phen
multic/inst/examples/solarOutput/pedindex.cde
multic/inst/examples/solarOutput/pedindex.out
multic/inst/examples/swOutput
multic/inst/examples/swOutput/IBD-18.013.gz
multic/inst/examples/swOutput/IBD-18.011.gz
multic/inst/examples/swOutput/IBD-18.003.gz
multic/inst/examples/swOutput/IBD-18.008.gz
multic/inst/examples/swOutput/IBD-18.019.gz
multic/inst/examples/swOutput/c18.map
multic/inst/examples/swOutput/IBD-18.009.gz
multic/inst/examples/swOutput/IBD-18.015.gz
multic/inst/examples/swOutput/IBD-18.012.gz
multic/inst/examples/swOutput/IBD-18.004.gz
multic/inst/examples/swOutput/IBD-18.018.gz
multic/inst/examples/swOutput/IBD-18.002.gz
multic/inst/examples/swOutput/IBD-18.005.gz
multic/inst/examples/swOutput/IBD-18.017.gz
multic/inst/examples/swOutput/IBD-18.016.gz
multic/inst/examples/swOutput/IBD-18.010.gz
multic/inst/examples/swOutput/IBD-18.007.gz
multic/inst/examples/swOutput/IBD-18.006.gz
multic/inst/examples/swOutput/IBD-18.014.gz
multic/inst/examples/swOutput/IBD-18.001.gz
multic/inst/examples/calls.q
multic/inst/docs
multic/inst/docs/multicTechReport.pdf
multic/src
multic/src/Lib.h
multic/src/Makevars
multic/src/Rostream.h
multic/src/Least.h
multic/src/Calculate.cpp
multic/src/Maxfun_add.cpp
multic/src/loadVarSandwich.cpp
multic/src/Rstreambuf.cpp
multic/src/verS.h
multic/src/Composite.cpp
multic/src/sortIdPairs.cpp
multic/src/multicString.cpp
multic/src/loadEffects.cpp
multic/src/loadVMatrixFile.cpp
multic/src/Maxfun_source.cpp
multic/src/getShareOutOrder.cpp
multic/src/Estimator.h
multic/src/Calculate.h
multic/src/ReadFamilyData.h
multic/src/Maxfun.cpp
multic/src/loadInvExpSecDerRandom.cpp
multic/src/splitTempMloci.cpp
multic/src/TraitMarkerCov_par.h
multic/src/solar2mloci.cpp
multic/src/Robust_Variance.cpp
multic/src/fixibd.cpp
multic/src/extractLoci.cpp
multic/src/getFamilySizes.cpp
multic/src/Least.cpp
multic/src/Robust_Variance.h
multic/src/ReadFamilyData.cpp
multic/src/Likelihoodfun.h
multic/src/Maxfun_add.h
multic/src/Vector.cpp
multic/src/loadFamilyLogLikelihoods.cpp
multic/src/multic.cpp
multic/src/Likelihoodfun.cpp
multic/src/Maxfun_source.h
multic/src/Lib.cpp
multic/src/sw2mloci.cpp
multic/src/calculateCorrelations.cpp
multic/src/Maxfun_fun.h
multic/src/fullId.cpp
multic/src/isSpouse.cpp
multic/src/makeBlockIdPair.cpp
multic/src/Composite.h
multic/src/Rstreambuf.h
multic/src/getResidualPlacement.cpp
multic/src/multicString.h
multic/src/Maxfun.h
multic/src/InitValue_par.cpp
multic/src/InitValue_par.h
multic/src/ShrinkData.h
multic/src/validateShareOut.cpp
multic/src/Vector.h
multic/src/Model.cpp
multic/src/multic.h
multic/src/ShrinkData.cpp
multic/src/loadYBetaDiffFile.cpp
multic/src/Model.h
multic/src/TraitMarkerCov_par.cpp
multic/NAMESPACE
multic/R
multic/R/plot.multic.q
multic/R/print.multic.q
multic/R/load.inv.exp.sec.der.fixed.q
multic/R/subsets.q
multic/R/load.inv.exp.sec.der.random.q
multic/R/matplot.multic.q
multic/R/multic.utilities.q
multic/R/multic.q
multic/R/solar2multic.q
multic/R/load.effects.q
multic/R/fixibd.q
multic/R/get.max.lod.and.locus.q
multic/R/solar2mloci.q
multic/R/addGE.q
multic/R/mlociCut.q
multic/R/print.summary.multic.q
multic/R/add.heritability.q
multic/R/merlin2mloci.q
multic/R/fitted.multic.q
multic/R/herit.se.q
multic/R/load.residuals.q
multic/R/phi2share.q
multic/R/load.v.matrices.q
multic/R/summary.multic.q
multic/R/sw2mloci.q
multic/R/pchisq.mix.q
multic/R/gene.eff.q
multic/R/expand.multic.q
multic/R/zzz.q
multic/R/load.var.sandwich.q
multic/R/get.top.n.families.q
multic/R/t.rank.q
multic/R/load.y.beta.diffs.q
multic/R/residuals.multic.q
multic/R/plot.family.lods.q
multic/R/polygene.q
multic/MD5
multic/README
multic/DESCRIPTION
multic/man
multic/man/solar2mloci.Rd multic/man/subsets.Rd multic/man/multic.Rd multic/man/expand.data.Rd multic/man/sw2mloci.Rd multic/man/plot.multic.Rd multic/man/plot.family.lods.Rd multic/man/phi2share.Rd multic/man/solar2multic.Rd multic/man/multic.object.Rd multic/man/summary.multic.Rd multic/man/t.rank.Rd multic/man/non.user.level.objects.Rd multic/man/expand.multic.Rd multic/man/multic.control.Rd multic/man/addGE.Rd multic/man/print.multic.Rd
multic/LICENSE
multic/CHANGES

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

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