maanova-internal {maanova}R Documentation

Internal maanova functions

Description

Internal maanova functions. These are generally not to be called by the user.

Usage

JS(X, var)
JSshrinker(X, df, meanlog, varlog)
buildtree(ct, binstr, depth, parent, idx.node, idx.leave)
calPval(fstar, fobs, pool)
calVolcanoXval(matestobj)
caldf(model, term)
check.confounding(model, term1, term2)
checkContrast(model, term, Contrast)
cluster2num(clust)
consensus.hc(macluster, level, draw)
consensus.kmean(macluster, level, draw)
dist.cor(x)
findgroup(varid, ndye)
getPval.volcano(matestobj, method, idx)
glowess(object, method, f, iter, degree, draw)
intprod(terms, intterm)
linlog(object, cg, cr, draw)
linlog.engine(data, cutoff)
linlogshift(object, lolim, uplim, cg, cr, n.bin, draw)
locateTerm(labels, term)
make.ratio(object, norm.std=TRUE)
makeAB(ct, coord, treeidx, startx, maxdepth)
makeCompMat(n)
makeD(s20, dimZ)
makeDesign(design)
makeHq(s20, y, X, Z, Zi, ZiZi, dim, b, method)
makeShuffleGroup(sample.mtx, ndye, narray)
makeZiZi(Z, dimZ)
makelevel(model, term)
matest.engine(anovaobj, term, mv, test.method, Contrast,
              is.ftest, partC, verbose=FALSE)
matest.perm(n.perm, FobsObj, data, model, term, Contrast, 
            mv, is.ftest, partC, MME.method, test.method,
            shuffle.method, pool.pval, ngenes)
meanvarlog(df)
## S3 method for class 'consensus.hc'
plot(x, title, ...)
## S3 method for class 'consensus.kmean'
plot(x, ...)
## S3 method for class 'madata'
print(x, ...)
## S3 method for class 'summary.mamodel'
print(x, ...)
ratioVarplot(logsum, logdiff, n)
rlowess(object, method, grow, gcol, f, iter, degree, draw)
shift(object, lolim, uplim, draw)
shuffle.maanova(data, model, term)
solveMME(s20, dim, XX, XZ, ZZ, a)
## S3 method for class 'madata'
summary(object, ...)
## S3 method for class 'mamodel'
summary(object, ...)
volcano.ftest(matestobj, threshold, method, title,highlight.flag)
volcano.ttest(matestobj, threshold, method, title,highlight.flag,
   onScreen)
matsort(mat, index=1)
repmat(mat, n.row, n.col, ...)
zeros(dim)
ones(dim)
blkdiag(...)
rowmax(x)
rowmin(x)
colmax(x)
colmin(x)
sumrow(x)
matrank(X)
norm(X)
mixed(y, X, Z, XX, XZ, ZZ, Zi, ZiZi, dimZ, s20, method =
      c("noest", "MINQE-I", "MINQE-UI", "ML", "REML"),
      maxiter = 100)
parseformula(formula, random, covariate)
makeContrast(model, term)
pinv(X, tol)
ma.svd(x, nu=min(n,p), nv=min(n,p), method=c("dgesvd","dgesdd"))
fdr(p, method = c("stepup", "adaptive", "stepdown", 'jsFDR'))

Details

Some funtion descriptions are:

Author(s)

Hao Wu; Hyuna Yang, hyuna.yang@jax.org

Examples

# for matsort
a<-matrix(c(1,6,4,3,5,2),2,3)
matsort(a,1)
matsort(a,2)

# for ones and zeros
ones(c(2,2))
zeros(c(2,3,2))

# for repmat
a<-c(1,2)
repmat(a,2,1)
a<-matrix(1:4,2,2)
repmat(a,1,2)

# for blkdiag
a<-matrix(1:4,2,2)
b<-matrix(3:6,2,2)
blkdiag(a,b)
blkdiag(a,b,c(1,2))

# others examples are omitted


[Package maanova version 1.30.0 Index]