Nothing
#======================================================================================================
#
# multiData.eigengeneSignificance
#
#======================================================================================================
multiData.eigengeneSignificance = function(multiData, multiTrait, moduleLabels,
multiEigengenes = NULL,
useModules = NULL,
corAndPvalueFnc = corAndPvalue, corOptions = list(),
corComponent = "cor", getQvalues = FALSE,
setNames = NULL, excludeGrey = TRUE,
greyLabel = ifelse(is.numeric(moduleLabels), 0, "grey"))
{
corAndPvalueFnc = match.fun(corAndPvalueFnc);
size = checkSets(multiData);
nSets = size$nSets;
nGenes = size$nGenes;
nSamples = size$nSamples;
if (is.null(multiEigengenes)) {
multiEigengenes = multiSetMEs(multiData, universalColors = moduleLabels, verbose = 0,
excludeGrey = excludeGrey, grey = greyLabel);
} else {
eSize = checkSets(multiEigengenes);
if (!isTRUE(all.equal(eSize$nSamples, nSamples)))
stop("Numbers of samples in multiData and multiEigengenes must agree.");
}
if (!is.null(useModules))
{
keep = substring(colnames(multiEigengenes[[1]]$data), 3) %in% useModules;
if (sum(keep)==0)
stop("Incorrectly specified 'useModules': no such module(s).");
if (any( ! (useModules %in% substring(colnames(multiEigengenes[[1]]$data), 3))))
stop("Some entries in 'useModules' do not exist in the module labels or eigengenes.");
for (set in 1:nSets)
multiEigengenes[[set]]$data = multiEigengenes[[set]]$data[, keep, drop = FALSE];
}
modLevels = substring(colnames(multiEigengenes[[1]]$data), 3);
nModules = length(modLevels);
MES = p = Z = nObs = array(NA, dim = c(nModules, nSets));
haveZs = FALSE;
for (set in 1:nSets)
{
corOptions$x = multiEigengenes[[set]]$data;
corOptions$y = multiTrait[[set]]$data;
cp = do.call(corAndPvalueFnc, args = corOptions);
corComp = grep(corComponent, names(cp));
pComp = match("p", names(cp));
if (is.na(pComp)) pComp = match("p.value", names(cp));
if (is.na(pComp)) stop("Function `corAndPvalueFnc' did not return a p-value.");
MES[, set] = cp[[corComp]]
p[, set] = cp[[pComp]];
if (!is.null(cp$Z)) { Z[, set] = cp$Z; haveZs = TRUE}
if (!is.null(cp$nObs))
{
nObs[, set] = cp$nObs;
} else
nObs[, set] = t(is.na(multiEigengenes[[set]]$data)) %*% (!is.na(multiTrait[[set]]$data));
}
if (is.null(setNames))
setNames = names(multiData);
if (is.null(setNames))
setNames = spaste("Set_", c(1:nSets));
colnames(MES) = colnames(p) = colnames(Z) = colnames(nObs) = setNames;
rownames(MES) = rownames(p) = rownames(Z) = rownames(nObs) = colnames(multiEigengenes[[1]]$data);
if (getQvalues)
{
q = apply(p, 2, qvalue.restricted);
dim(q) = dim(p);
dimnames(q) = dimnames(p);
} else q = NULL;
if (!haveZs) Z = NULL;
list(eigengeneSignificance = MES,
p.value = p,
q.value = q,
Z = Z,
nObservations = nObs)
}
#==============================================================================================
#
# nSets
#
#==============================================================================================
nSets = function(multiData, ...)
{
size = checkSets(multiData, ...);
size$nSets;
}
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