Man pages for drmjc/metaGSEA
Meta-analysis of GSEA analyses, including intra- and inter-experiment comparisons

affy.pivot.tablemerge expression and calls together
average.replicates.gctAverage replicate columns from within a gct file Average...
catplot.GSEAFunction to generate CAT plots for >= 2 GSEA comparisons
catplot.GSEA.2wayPlot a CAT plot upon 2 GSEA objects.
catplot.GSEA.2way.vs.randomCompare 2 GSEA runs via CAT plots & estimate the expected...
catplot.GSEA.randomCompare multiple GSEA runs via CAT plots & estimate the...
chip2descriptionConvert a GSEA chip file or object into a vector of...
collapse.gctCollapse a GCT object
collapse.gct2genesetCollapse a GCT file from 1 row per gene to 1 row per geneset.
collapse.gct.fileCollapse a GCT file
convert.gct2submapPrepare data for use in SubMap.
convert.gsea.res2gctConvert a res object to a gct object.
dist.gseaDetermine the distance between various leading edge genes, in...
export.broad.clsExport a cls file for GenePattern. Export a cls file for...
export.broad.resExport a res file for GenePattern.
export.gseaExport a gsea object to the filesystem.
export.gsea.cdtCluster leading edge genesets, and export in Stanford cdt/gtr...
export.gsea.chipExport a GSEA chip file Export a GSEA chip file - this...
export.gsea.edbExport a GSEA edb object to an 'XML' file.
export.gsea.gctFunction to export a GenePattern gct file.
export.gsea.gct.topTableExport a GCT file, from a GSEA topTable plus data table
export.gsea.gmtExport a gmt file Genesets for BROAD's GSEA are usually...
export.gsea.gtrYou should use export.gsea.cdt instead.
export.gsea.leadingedge.analysisExport the plots and tables required for a GSEA leading edge...
export.gsea.odfExport a table of data to a GenePattern odf file
export.gsea.odf.lmFitExport a limma lmFit to a GSEA ODF file. From two linear...
export.gsea.rnkExport a vector of values as a GSEA pre-ranked list.
export.gsea.rnk.topTableExport a limma topTable to a GSEA pre-ranked list. The 'rnk'...
export.gsea.rptExport a GSEA rpt file
genepattern2spdGenePattern to SPD
genepattern.HeatMapImageFrom a GCT file, create a HeatMap Image, using the jar from...
GMThyperGTestPerform a Hypergeometric test, upon a GMT file. Much like...
gsea2adjmatConvert a GSEA object into an adjacency matrix at the...
gsea.combineCombine N gsea runs together
gsea.compare.runs.1gmtCompare N GSEA runs vs a single gmt file (eg lots of rnk...
gsea.compare.runs.filterFunction to filter a set of GSEA run comparisons, and/or to...
gsea.compare.runs.sortFunction to sort the rows of a GSEA comparison object
gsea.convert.clm2clsConvert a clm file into a cls file.
gsea.filterTake a GSEA list, and filter out genesets that fail various...
gsea.filter.edbFilter a GSEA edb file, restricting the entries to restricted...
gsea.fix.outputFix the output from a GSEA run
gsea.fix.output.detailed.enrichment.results.htmlfix the "Detailed enrichment results in html format" 2 pages.
gsea.fix.output.geneset.reportfix an individual GSEA GeneSet html report.
gsea.fix.output.index.htmlfix the index.html file
gsea.gct.probes2genesConvert probe-level to gene-level gct
gsea.gct.select.features.columnsRestrict the number of columns in a gct & cls file.
gsea.gct.select.features.rowsSubset the rows of a gct file. The GenePattern...
gsea.genesets2gctCreate gct files for all gseaPreranked runs comparing 1 rnk...
gsea.hardwire.rpt.pathsRewire the file locations referenced within a GSEA rpt file.
GSEAhyperGTestPerform a Hypergeometric test, upon a GMT file. This is a...
gsea.leadingedge.distanceDetermine the distance between various leading edge genes, in...
gsea.lengthHow many genesets in a GSEA object?
gsealist2adjmatConvert a GSEA list into an adjacency matrix at the...
gsealist2genesetlistExtract the geneset names from a list of GSEA objects.
gsealist.find.genesetFrom a list of GSEA's, find the elements that contain...
gsea.mergeMerge two GSEA objects.
gsea.merge.dirsMerge 2 gsea runs, by referencing only the GSEA directories.
gsea.merge.edbMerge two GSEA edb objects.
gsea.merge.edb.dirsFunction to merge the edb files from 2 GSEA runs.
gsea.merge.ttMerge N GSEA toptables, retaining a column of interest (eg...
gsea.rename.genesetsRename the genesets from within a GSEA object.
gsea.rename.genesets.edbParse an edb XML object, and rename the genesets with...
gsea.reorder.gmt.by.rnkReorder the genes within a gmt object to match the order of...
gsea.splitSplit a GSEA object based on leading edge similarities. Take...
gsea.summariseSummarise GSEA results
gsea.topTable.sortsort a GSEA topTable
gsea.which.gmtWhat gmt file was used?
import.genepattern.odfimport.genepattern.odf
import.gseaImport the results from a GSEA or GseaPreRanked analysis.
import.gsea.chipImport a GSEA chip file. This can look inside a gsea output...
import.gsea.clmImport a clm file
import.gsea.clsImport a cls file
import.gsea.compare.runsImport the output produced by gsea.compare.runs.sh
import.gsea.edbImport a GSEA edb file. The edb file is a machine readable...
import.gsea.gctImport a gct file
import.gsea.gmtImport a gmt file that is commonly used by Broad's GSEA.
import.gsea.gmxImport a gmx file that is commonly used by Broad's GSEA.
import.gsea.leadingedgeImport the leading edge subset of genes from each category....
import.gsea.resImport a GenePattern res file
import.gsea.rnkImport a rnk file used for running GSEA PreRanked.
import.gsea.rptImport the rpt file from a GSEA, or GseaPreRanked analysis...
import.gsea.topTableImport the tabular results from a GSEA PreRanked run
is.gseaIs x a GSEA object
is.gsea.diris the argument a valid GSEA directory?
is.gsea.gct.fileis.gsea.gct.file
is.gsea.listis 'x' a gsea list, that is, a list containing gsea results?
is.gsea.res.fileis.gsea.res.file
is.gsea.zipIs the argument a GSEA zip file?
jacquard-methodsThe Jacquard coefficient as a measure of overlap in terms of...
metaGSEA-packageMeta-analysis of GSEA analyses, including intra- and...
plclust.gseaPlot an hclust object, that has been made from GSEA genesets.
plclust_in_colourmodifiction of plclust for plotting hclust objects *in...
plot_gseacmp.barplotTaking a gseacmp object (see gsea.compare.runs.1gmt), create...
plot_gsea.leadingedgeCombination GSEA Leading Edge plot.
plot_gsea.leadingedge.adjmatGenerate a binary adjacency matrix image (like a heatmap with...
plot_gsea.leadingedge.barplotGSEA Leading Edge analysis: Barplot of number of genesets...
plot_gsea.leadingedge.barplot.autoFunction to automatically plot barplot's of filtered GSEA...
plot_gsea.leadingedge.HCLGSEA Leading Edge HCL plot.
plot_gsea.leadingedge.HCL.1clusterPerPageTake a GSEA object, do an HCL between the leading edge genes,...
plot_gsea.leadingedge.HCL.autoAutomated GSEA HCL
plot_gsea.leadingedge.HCL.simpleTake a GSEA object and calculate an HCL between the leading...
plot_gsea.leadingedge.heatmapGenerate a heatmap of genesets from a GSEA run
plot_gsea.leadingedge.heatmap.autoGenerate a heatmap of genesets from a GSEA run, across a...
plot_gsea.resBoxplot the intensities for an array split by the detection...
plot_gsea.statistic.histogramsplot a panel of gsea histograms From a GSEA object, plot a...
plot_gsea.vennCompare the significant genesets from 2 or 3 GSEA runs using...
plot_gsea.venn.autoPlot a Venn diagram of overlaps between genesets from >= 2...
print.gsea.vennPrint a Venn diagram of overlaps between genesets from >= 2...
qplot.data.qplot.data This code is taken from qvalue::qplot (from...
reorder.gctFunction to reorder the rows of a GCT object
reorder.gct.fileReorder the rows of a GCT file.
subset.gseaSubsetting GSEA objects. Return subsets of GSEA objects which...
test.broad.ftptest whether a connection to BROAD's FTP/HTTP sites can be...
drmjc/metaGSEA documentation built on May 15, 2019, 2:24 p.m.