Meta-Analysis of MicroArray

clinical | Functions to retrieve and assign |

clinical.sum | Function to calculate summaries of clinical data |

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... |

computeAlpha | Function to do compute tunning parameter alpha |

computeOrdering | Function to compute ordered gene lists |

compute.RQ | Function to compute R and Q statistics as defined in - see... |

conting.tab | Contingency table from gene lists |

cv.filter | Microarray probes filtering |

entitybuild2 | Function to calculate test statistic for microarray data |

ES.GeneMeta | Wrapper function for combining the effect size as implemented... |

flip | Function to flip data frames |

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... |

join.results | Function to join results from meta-analysis to one list |

make.matrix | Function to make matrix for heatmap to compare results of... |

MAP.genes | Function to do assign probesets IDs to patterns |

MAP.Matches | 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 |

MetaArray | 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... |

meta.test | Function to compute T-statistic and p-value in meta-analysis |

methods | Replacement Methods for 'MetaArray' object |

METRADISC | Wrapper function for METRADISC method |

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... |

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... |

plot.SOGLresult | Function to plot an object of class SOGLresult |

prelimScore | Function compute preliminary Similarity Score for Ordered... |

prepareData | Function to prepare data |

preparePermutations | Function to prepare permutation and subsamples |

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 |

ratio | Function to calculate the ratio of co-significant:... |

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 |

sigScore | Function to calculate signifficance of similarity score |

test.group.shuffle | Function to do compute test statistic iterativelly |

T.select | Function to help with selection of threshold for T-statistics |

VennMapper | Wrapper function for VennMapping |

Z | Function to compute Z-statistics in contingency table |

zScores | Function for Meta-analysis of gene expression data |

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