Quantitative linkage analysis tools using the variance components approach

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Documentation for package ‘multic’ version 0.3.2

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A C E F G H I L M N P R S T U V W misc

-- A --

add.heritability This function is not intended for user-level use.
addGE Assess combinations of univariate multic objects
all.equal.multic This function is not intended for user-level use.
apply.sequential.ids This function is not intended for user-level use.

-- C --

calculate.coefficients This function is not intended for user-level use.
calculate.cor.values This function is not intended for user-level use.
calculate.correlations This function is not intended for user-level use.
calculate.descriptives This function is not intended for user-level use.
calculate.initial.values This function is not intended for user-level use.
canonical.path.name This function is not intended for user-level use.
check.data.for.missing.values This function is not intended for user-level use.
check.for.full.data This function is not intended for user-level use.
clean This function is not intended for user-level use.
collapseMibd This function is not intended for user-level use.
combine.null.and.alt.initial.values This function is not intended for user-level use.
copy This function is not intended for user-level use.
copy.files.to.tmp.space This function is not intended for user-level use.
create.multic.object This function is not intended for user-level use.

-- E --

expand.data Create a "bootstrapped" version of a dataset to be used in multic.
expand.locus This function is not intended for user-level use.
expand.mloci This function is not intended for user-level use.
expand.multic Create "bootstrapped" versions of mloci.out and share.out for multic
expand.share This function is not intended for user-level use.
expandMibd This function is not intended for user-level use.

-- F --

fitted.multic This function is not intended for user-level use.
fixibd This function is not intended for user-level use.
formula.multic This function is not intended for user-level use.

-- G --

gene.eff This function is not intended for user-level use.
get.basename This function is not intended for user-level use.
get.cm.close.to.peak This function is not intended for user-level use.
get.cM.from.v.mat This function is not intended for user-level use.
get.covariance.indices This function is not intended for user-level use.
get.df.mix This function is not intended for user-level use.
get.dist This function is not intended for user-level use.
get.extension This function is not intended for user-level use.
get.family.count This function is not intended for user-level use.
get.family.parent.inconsistancies This function is not intended for user-level use.
get.family.sizes This function is not intended for user-level use.
get.major.diagonal.indices This function is not intended for user-level use.
get.max.lod.and.locus This function is not intended for user-level use.
get.n This function is not intended for user-level use.
get.p.mix This function is not intended for user-level use.
get.share.order This function is not intended for user-level use.
get.top.n.families This function is not intended for user-level use.
get.unique.families This function is not intended for user-level use.
get.var.covar.labels This function is not intended for user-level use.
get.variances.from.file This function is not intended for user-level use.
gunzip This function is not intended for user-level use.
gzip This function is not intended for user-level use.

-- H --

herit.se This function is not intended for user-level use.

-- I --

is.multic This function is not intended for user-level use.
is.parent.offspring This function is not intended for user-level use.
is.sibling This function is not intended for user-level use.
is.spouse This function is not intended for user-level use.

-- L --

lappend This function is not intended for user-level use.
lm.ready.check This function is not intended for user-level use.
load.effects This function is not intended for user-level use.
load.family.log.likelihoods This function is not intended for user-level use.
load.inv.exp.sec.der.fixed This function is not intended for user-level use.
load.inv.exp.sec.der.random This function is not intended for user-level use.
load.iterations This function is not intended for user-level use.
load.residuals This function is not intended for user-level use.
load.v.matrices This function is not intended for user-level use.
load.v.matrix.file This function is not intended for user-level use.
load.var.sandwich This function is not intended for user-level use.
load.y.beta.diffs This function is not intended for user-level use.
load.y.beta.file This function is not intended for user-level use.

-- M --

make.block.id.pair This function is not intended for user-level use.
make.kinship.file This function is not intended for user-level use.
max.multic This function is not intended for user-level use.
mergeWithKinship This function is not intended for user-level use.
missing.value This function is not intended for user-level use.
mloci.split This function is not intended for user-level use.
mlociCut This function is not intended for user-level use.
multic Create a multic object
multic.colnames This function is not intended for user-level use.
multic.control Set control parameters for multic
multic.is.dir This function is not intended for user-level use.
multic.kurtosis This function is not intended for user-level use.
multic.mkdir This function is not intended for user-level use.
multic.object a multic object
multic.rownames This function is not intended for user-level use.
multic.skewness This function is not intended for user-level use.
multic.strings.split This function is not intended for user-level use.
multic.strsplit This function is not intended for user-level use.
multic.system This function is not intended for user-level use.
multic.unlink This function is not intended for user-level use.

-- N --

non.user.level.objects This function is not intended for user-level use.
normalize.mibd This function is not intended for user-level use.

-- P --

parse.trait.names This function is not intended for user-level use.
pchisq.mix This function is not intended for user-level use.
phi2share Convert a SOLAR-formatted phi2 file into a multic-formatted share.out file.
plot.family.lods Plot family contribution to peak LOD
plot.multic Plot a multic object
polygene This function is not intended for user-level use.
print.multic Use print() on a multic object
print.summary.multic This function is not intended for user-level use.

-- R --

read.pedindex.out This function is not intended for user-level use.
recover.multic This function is not intended for user-level use.
remove.file This function is not intended for user-level use.
remove.temp.files This function is not intended for user-level use.
residuals.multic This function is not intended for user-level use.
run.alternative.multic This function is not intended for user-level use.

-- S --

solar2mloci Convert a directory of SOLAR-formatted ibd and/or mibd files into a multic-formatted mloci.out
solar2multic Convert SOLAR-formatted output into multic-formatted mloci.out and share.out
sortIbdCols This function is not intended for user-level use.
subsets Choose Sets Of Size k From The n-Elements Of a Vector
summary.multic This function is not intended for user-level use.
sw2mloci Convert SimWalk IBD files into a single mloci.out.

-- T --

t.rank Empirical Normal Quantile transformation
trim This function is not intended for user-level use.

-- U --

upp.tri.as.vector This function is not intended for user-level use.
using.R This function is not intended for user-level use.

-- V --

validate.parents This function is not intended for user-level use.
validate.share.out This function is not intended for user-level use.

-- W --

write.alt.initial.values This function is not intended for user-level use.
write.initial.values This function is not intended for user-level use.

-- misc --

[.multic This function is not intended for user-level use.