backwardSearch |
Backward Search Function |
calcMetaPower |
Calculates the statistical power of a random effects meta-analysis |
calculateROC |
Calculate ROC Curve Statistics |
calculateScore |
Calculate a signature Z-score for a set of genes in a single dataset |
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 objects. |
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 meta-analysis |
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 meta-analysis |
heatmapPlot |
Generates a heatmap with effect sizes for all genes which pass a filter in all measured diseases |
immunoStatesDecov |
immunoStates deconvolution analysis on MetaIntegrator object(s) |
immunoStatesGenePropCorr |
Correct gene expression using cell proportions from immunoStates |
immunoStatesMatrix |
immunoStates basis matrix |
immunoStatesMeta |
immunoStates deconvolution analysis on MetaIntegrator object(s) |
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 |
MetaIntegrator package for meta-analysis of gene expression data |
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 prevalences |
regressionPlot |
Generate a plot which draws a regression line between the Meta Score and a continuous variable phenotype. |
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 |