Man pages for MetaIntegrator
Meta-Analysis of Gene Expression Data
| backwardSearch | Backward Search Function |
| calcMetaPower | Calculates the statistical power of a random effects... |
| calculateROC | Calculate ROC Curve Statistics |
| calculateScore | Calculate a signature Z-score for a set of genes in a single... |
| checkDataObject | Check for errors in objects used for analysis |
| classFunction | Helper function to build the class vector |
| cleanUpPheno | Automatic preprocessing of $pheno dataframe |
| coconutMetaIntegrator | A wrapper function to run COCONUT on the MetaIntegrator... |
| ens_ensgID_table | ENSEMBL gene id table cache |
| ens_entrez_table | ENSEMBL entrez table cache |
| filterGenes | Filter out significant genes from meta-analysis results |
| forestPlot | Compare effect sizes of a gene across all datasets in... |
| forwardSearch | Forward Search Function |
| geneSymbolCorrection | Correct/update gene symbols in a metaObject |
| getGEOData | GEO download/processing through GEOquery |
| getMostRecentFilter | Get name of most recent filter |
| getSampleLevelGeneData | Extract gene-level data from a given data object |
| ggForestPlot | Compare effect sizes of a gene across all datasets in... |
| heatmapPlot | Generates a heatmap with effect sizes for all genes which... |
| immunoStatesDecov | immunoStates deconvolution analysis on MetaIntegrator... |
| immunoStatesGenePropCorr | Correct gene expression using cell proportions from... |
| immunoStatesMatrix | immunoStates basis matrix |
| immunoStatesMeta | immunoStates deconvolution analysis on MetaIntegrator... |
| imputeSex | Imputes biological sex of each sample in a Dataset object |
| lincsBaitCorr | Run Shane's LINCS bait-based correlation on MetaIntegrator |
| lincsCorrelate | Run Shane's LINCS Correlate on MetaIntegrator |
| lincsTools | Run Shane's LINCS Tools on MetaIntegrator |
| manhattanPlot | Generates a Manhattan plot with effect size FDR as y-axis |
| metaIntegrator_public-package | MetaIntegrator package for meta-analysis of gene expression... |
| multiplePRCPlot | Generate a plot with multiple PRC curves |
| multipleROCPlot | Generate a plot with multiple ROC curves |
| pooledROCPlot | Generate a plot with a pooled ROC curve |
| prcPlot | Plot the PRC Curve for a Dataset |
| predvalPlot | Plot positive and negative predictive values across different... |
| regressionPlot | Generate a plot which draws a regression line between the... |
| rocPlot | Plot ROC Curve for a Dataset |
| runMetaAnalysis | Run the meta-analysis algorithm |
| subsetOriginalData | Subset samples for a particular dataset |
| summarizeFilterResults | Summarize the filtered analysis results |
| summaryROCCalc | Calculate the summaryROC statistics |
| summaryROCPlot | Generate a plot with a summary ROC curve |
| tinyMetaObject | A Tiny MetaObject |
| ucsc_genbank_table | UCSC genbank table cache |
| ucsc_refseq_table | UCSC refseq table cache |
| violinPlot | Compare groups within a single dataset in a violin plot |
