This package builds on the Epimods framework which facilitates finding weighted subnetworks ("modules") on Illumina Infinium 27k arrays using the SpinGlass algorithm, as implemented in the iGraph package. We have created a class of gene centric annotations associated with p-values and effect sizes and scores from any researchers prior statistical results to find functional modules.
|Author||Neil Ari Wijetunga, Andrew Damon Johnston, John Murray Greally|
|Date of publication||None|
|Maintainer||Neil Ari Wijetunga <Neil.Wijetunga@med.einstein.yu.edu>, Andrew Damon Johnston <Andrew.Johnston@med.einstein.yu.edu>|
addShadowText: Add shadow text (a second color bordering the text) to a plot
annotateExpression: Adding expression data to a PvalueAnnotation
annotateModification: Adding modification data to a PvalueAnnotation
convertGeneIds: Convert between gene ids
curated_expression: A toy dataset ofcurated RNA-seq to test within SMITE
extractExpression: View the expression data stored in a PvalueAnnotation
extractGOseq: View the GOseq pathway analysis after having run Goseq, or...
extractModification: Extract some or all loaded modifications or a the summary of...
extractModules: View specific modules within a PvalueAnnotation
extractScores: Extract scores for all genes
genes_for_conversiontest: A small set of RefSeq genes for converting
hg19_gene_bed: A bed file annotating Refseq genes for the hg19 genome build
highScores: Generate a vector of the highest scoring genes
histone_h3k4me1: A toy dataset of H3k4me1 peaks to test within SMITE
makePvalueAnnotation: Initialize a PvalueAnnotation
makePvalueObject: Function to make a PvalueObject within a PvalueAnnotation
methylationdata: A toy dataset of DNA methylation to test within SMITE
normalizePval: This function normalizes p-values (Scores) that are otherwise...
plotCompareScores: Compare two genomic features by score and display them in a...
plotDensityPval: Plot the density of the combined scores stored in a...
plotModule: Plot a specific module after running Spinglass algorithm
Reactome.Symbol.Igraph: An Igraph network for REACTOME with nodes as gene symbols
removeModification: A function to "unload" a modification that has already been...
runBioNet: Perform BioNet Analysis on a PvalueAnnotation
runGOseq: Run a GoSeq pathway analysis
runSpinglass: Run Spinglass algorithm on a Scored PvalueAnnotation
scorePval: Making a single combined score for each gene
SMITE-package: Significance-based Modules Integrating the Transcriptome and...
stoufferTest: Stouffer's Test
test_annotation_score_data: A toy PvalueAnnotation