compute.RQ |
Function to compute R and Q statistics as defined in - see References |
conting.tab |
Contingency table from gene lists |
cv.filter |
Microarray probes filtering |
dataGEM |
Data format converter |
dataSOGL |
Data format converter |
dataZ |
Data format converter |
entitybuild2 |
Function to calculate test statistic for microarray data |
fold.change |
function to do compute fold change between two groups |
gene.list |
Intersect of gene lists |
gene.select.FC |
Function to select genes according to fold change |
join.DEG |
Function to join vectors of differentially expressed genes to one list |
join.results |
Function to join results from meta-analysis to one list |
make.matrix |
Function to make matrix for heatmap to compare results of several methods |
MAP.genes |
Function to do assign probesets IDs to patterns |
MAP.HTMLanno |
Function to do make annotation of vectors of probeset ID |
MAPmatrix |
Function to summarize binary matrix |
MAPsig1 |
Pattern signifficance |
MAPsig2 |
Pattern signifficance |
MCtest |
Monte Carlo permutation test |
mergedata |
Function to do merge ExpressionSet objects |
meta.test |
Function to compute T-statistic and p-value in meta-analysis |
metagene |
Function to do extract row from list of data.frames |
metaheat |
Display Data as Heatmap |
metaheat2 |
Function to do plot heatmap |
metalist.to.matrix |
Function to do convert list to matrix |
patternMatch |
Function to count soft pattern matches |
patternMatch.strong |
Function to count strong pattern matches |
patternmatrix |
Function to split binary vectors to matrix. |
patternToString |
Function to convert rows of a matrix to strings |
plotclinical |
Plot of clinical variables |
plotES |
Function to do plots in combination of effect size method |
plotgene |
Function to visuaze change in expression of one gene |
plotpattern |
Function to do plot signifficance of Meta-Analysis Patterns |
plotQvsChi |
Function to plot quantiles of Cochran's Q statistic and Chi-square quantiles. |
probs.to.matrix |
Function to convert list to matrix |
rank.genes |
Rank genes |
rank.genes.adv |
Function to rank genes |
ratio |
Function to calculate the ratio of co-significant: expected/observed |
sd.filter |
Microarray probes filtering |
T.select |
Function to help with selection of threshold for T-statistics |
test.group.shuffle |
Function to do compute test statistic iterativelly |
Z |
Function to compute Z-statistics in contingency table |