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| as.list-method | Class "MetaArray" ~~~ |
| clinical | Functions to retrieve and assign |
| clinical.sum | Function to calculate summaries of clinical data |
| clinical<- | Functions to retrieve and assign |
| clinical<--method | Functions to retrieve and assign |
| clinical<--method | Replacement Methods for 'MetaArray' object |
| clinical<--methods | Replacement Methods for 'MetaArray' object |
| colIntersect | Function to find intersect in columns of a data.frame |
| ColonData | Example dataset for meta-analysis of microarray |
| commonGenes | Function to compute number of common genes in ordered gene lists |
| compute.RQ | Function to compute R and Q statistics as defined in - see References |
| computeAlpha | Function to do compute tunning parameter alpha |
| computeOrdering | Function to compute ordered gene lists |
| conting.tab | Contingency table from gene lists |
| cv.filter | Microarray probes filtering |
| datanames | Functions to retrieve and assign |
| datanames<- | Functions to retrieve and assign |
| datanames<--method | Functions to retrieve and assign |
| datanames<--method | Replacement Methods for 'MetaArray' object |
| datanames<--methods | Replacement Methods for 'MetaArray' object |
| entitybuild2 | Function to calculate test statistic for microarray data |
| ES.GeneMeta | Wrapper function for combining the effect size as implemented in GeneMeta package |
| ES.GeneMeta.res | Wrapper function for combining the effect size as implemented in GeneMeta package |
| flip | Function to flip data frames |
| fold.change | Function to do compute fold change between two groups |
| GEDM | Functions to retrieve and assign |
| GEDM<- | Functions to retrieve and assign |
| GEDM<--method | Functions to retrieve and assign |
| GEDM<--method | Replacement Methods for 'MetaArray' object |
| GEDM<--methods | Replacement Methods for 'MetaArray' object |
| 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.Matches | Wrapper function for MAP-Matches method |
| MAP.Matches.res | Wrapper function for MAP-Matches method |
| MAPmatrix | Function to summarize binary matrix |
| MAPsig1 | Pattern signifficance |
| MAPsig2 | Pattern signifficance |
| MCtest | Monte Carlo permutation test |
| mergedata | Function to merge data from MetaArray object |
| mergeExprs2 | Function to merge ExpressionSet object |
| meta.test | Function to compute T-statistic and p-value in meta-analysis |
| MetaArray-class | Class "MetaArray" ~~~ |
| metagene | Function to do extract row from list of data.frames |
| metaheat | Display Data as Heatmap |
| metaheat2 | Function to plot heatmap |
| metalist.to.matrix | Function to do convert list to matrix |
| metaMA | Wrapper function for effect size or p-value combination methods |
| metaMA.res | Wrapper function for effect size or p-value combination methods |
| METRADISC | Wrapper function for METRADISC method |
| METRADISC.res | Wrapper function for METRADISC method |
| multExpFDR | Function for Meta-analysis of gene expression data |
| 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 |
| performSOGL | Function to perform analysis using Similarity of Ordered Gene Lists |
| plot-method | Class "MetaArray" ~~~ |
| plot.SOGLresult | Function to plot an object of class SOGLresult |
| plotES | Function to do plots in combination of effect size method |
| plotgene | Function to visuaze change in expression of one gene |
| plotgene2 | 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. |
| posterior.mean | Function to calculate posterior mean differential expression |
| prelimScore | Function compute preliminary Similarity Score for Ordered Gene Lists |
| prepareData | Function to prepare data |
| preparePermutations | Function to prepare permutation and subsamples |
| print-method | Class "MetaArray" ~~~ |
| probs.to.matrix | Function to convert list to matrix |
| RandomScore | Function to do compute random and subsampled similarity score |
| rank.genes | Rank genes |
| rank.genes.adv | Function to rank genes |
| RankProduct | Wrapper function for RankProduct method |
| RankProduct.res | Wrapper function for RankProduct method |
| ratio | Function to calculate the ratio of co-significant: expected/observed |
| sd.filter | Microarray probes filtering |
| selectAlpha | Function to select the most optimal alpha parameter |
| selectClass | Function to select class labels from MetaArray object |
| selectGenes | Function to select genes that account for Similarity score |
| show-method | Class "MetaArray" ~~~ |
| sigScore | Function to calculate signifficance of similarity score |
| T.select | Function to help with selection of threshold for T-statistics |
| test.group.shuffle | Function to do compute test statistic iterativelly |
| VennMapper | Wrapper function for VennMapping |
| VennMapper.res | Wrapper function for VennMapping |
| Z | Function to compute Z-statistics in contingency table |
| zScoreFDR | Function for Meta-analysis of gene expression data |
| zScorePermuted | Function for Meta-analysis of gene expression data |
| zScores | Function for Meta-analysis of gene expression data |