multic: Quantitative Linkage Analysis Tools using the Variance Components Approach

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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.

Author
Eric Lunde, Mariza de Andrade, Beth Atkinson, Pat Votruba
Date of publication
2016-01-29 11:18:30
Maintainer
Pat Votruba <votruba.patrick@mayo.edu>
License
GPL (>= 2) | file LICENSE
Version
0.4.3.1

View on CRAN

Man pages

addGE
Assess combinations of univariate multic objects
expand.data
Create a "bootstrapped" version of a dataset to be used in...
expand.multic
Create "bootstrapped" versions of mloci.out and share.out for...
multic
Create a multic object
multic.control
Set control parameters for multic
multic.object
a multic object
non.user.level.objects
This function is not intended for user-level use.
phi2share
Convert a SOLAR-formatted phi2 file into a multic-formatted...
plot.family.lods
Plot family contribution to peak LOD
plot.multic
Plot a multic object
print.multic
Use print() on a multic object
solar2mloci
Convert a directory of SOLAR-formatted ibd and/or mibd files...
solar2multic
Convert SOLAR-formatted output into multic-formatted...
subsets
Choose Sets Of Size k From The n-Elements Of a Vector
summary.multic
Use print() on a multic object
sw2mloci
Convert SimWalk IBD files into a single mloci.out.
t.rank
Empirical Normal Quantile transformation

Files in this package

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