bapred-internal: Internal bapred functions

In bapred: Batch Effect Removal and Addon Normalization (in Phenotype Prediction using Gene Data)

Internal bapred functions

Description

Internal bapred functions.

Usage

Dt(rho) 
VarInflation(dta, Blist, maxnbfactors, dig) 
aprior(gamma.hat) 
avedistTwo(xb1, xb2) 
bivprob(rho, lower, upper = -lower, mean = 0) 
bprior(gamma.hat) 
build.design(vec, des = NULL, start = 2) 
design.mat(mod, numCov) 
diffexprmAfterBR(x, xbrlist, y, batch, batchessuited) 
emfahighdim(eps, nbf, minerr = 1e-06, maxiter = 100) 
extractAffybatch(inds, abo)
fuzzywilcox(x, y) 
it.sol(sdat, g.hat, d.hat, g.bar, t2, a, b, conv = 1e-04) 
kldistTwo(xb1, xb2) 
list.batch(mod) 
mypvcaBatchAssess(X, factordata, threshold) 
nbfactors(dta, maxnbfactors = 12, diagnostic.plot = FALSE, minerr = 0.001, 
  maxiter = 100) 
normalizeAffyBatchqntval(abatch, type = c("separate", "pmonly", "mmonly", "together")) 
normalizeqntadd(abo, qnt.scale)
normalizeqntadd2(x, qnt.scale)
normalizeqntval(x)
plotcomp(xp, groups, y, alpha, col = rainbow(length(groupsun)), 
  xlim, ylim, ...) 
postmean(g.hat, g.bar, n, d.star, t2) 
postvar(sum2, n, a, b) 
## S3 method for class 'combat'
print(x, ...) 
## S3 method for class 'fabatch'
print(x, ...) 
## S3 method for class 'meancenter'
print(x, ...) 
## S3 method for class 'noba'
print(x, ...) 
## S3 method for class 'qunormtrain'
print(x, ...) 
## S3 method for class 'ratioa'
print(x, ...) 
## S3 method for class 'ratiog'
print(x, ...) 
## S3 method for class 'rmatrain'
print(x, ...)
## S3 method for class 'standardize'
print(x, ...) 
## S3 method for class 'svatrain'
print(x, ...) 
sepscoreTwo(xb1, xb2, k = 10) 
skewdivTwo(xb1, xb2)
summarizeadd2(abo, probe.effects) 
summarizeval2(abo)

Details

These internal bapred functions are not usually called directly by the user.

bapred documentation built on June 22, 2022, 9:08 a.m.