Entry: A4
Aliases: A4
Keywords: internal
Description: A4
URL: ../../../library/SIM/html/A4.html

Entry: RESOURCERER.annotation.to.ID
Aliases: RESOURCERER.annotation.to.ID
Keywords: misc
Description: Link RESOURCERER annotation file to expression ID
URL: ../../../library/SIM/html/RESOURCERER.annotation.to.ID.html

Entry: SIM-package
Aliases: SIM-package SIM
Keywords: package
Description: Statistical Integration of Microarrays
URL: ../../../library/SIM/html/SIM-package.html

Entry: acgh.data
Aliases: acgh.data
Keywords: datasets
Description: Array-comparative genomic hybridization data example
URL: ../../../library/SIM/html/acgh.data.html

Entry: acgh.heatmap.with.heatmap
Aliases: acgh.heatmap.with.heatmap
Keywords: internal
Description: Function to plot the copy number data as heatmap along side the association heatmap
URL: ../../../library/SIM/html/acgh.heatmap.with.heatmap.html

Entry: adj.bhfdr
Aliases: adj.bhfdr
Keywords: internal
Description: Adjust p-values using the Benjamini-Hochberg method
URL: ../../../library/SIM/html/adj.bhfdr.html

Entry: adj.byfdr
Aliases: adj.byfdr
Keywords: internal
Description: Adjust p-values using the Benjamini-Yekutieli method
URL: ../../../library/SIM/html/adj.byfdr.html

Entry: assemble.data
Aliases: assemble.data
Keywords: misc
Description: Assemble the data to run the integrated analysis
URL: ../../../library/SIM/html/assemble.data.html

Entry: chrom.table
Aliases: chrom.table
Keywords: datasets
Description: Table with chromosome arm positions
URL: ../../../library/SIM/html/chrom.table.html

Entry: collapse.arms
Aliases: collapse.arms
Keywords: internal
Description: collapse.arms
URL: ../../../library/SIM/html/collapse.arms.html

Entry: collapse.bands
Aliases: collapse.bands
Keywords: internal
Description: collapse.bands
URL: ../../../library/SIM/html/collapse.bands.html

Entry: create.color.vector
Aliases: create.color.vector
Keywords: internal
Description: create.color.vector
URL: ../../../library/SIM/html/create.color.vector.html

Entry: expr.data
Aliases: expr.data
Keywords: datasets
Description: Expression data example
URL: ../../../library/SIM/html/expr.data.html

Entry: get.abs.start
Aliases: get.abs.start
Keywords: internal
Description: get.abs.start
URL: ../../../library/SIM/html/get.abs.start.html

Entry: get.indep.zscores
Aliases: get.indep.zscores
Keywords: internal
Description: A function to calculate mean associations
URL: ../../../library/SIM/html/get.indep.zscores.html

Entry: get.pvals
Aliases: get.pvals
Keywords: internal
Description: get.pvals
URL: ../../../library/SIM/html/get.pvals.html

Entry: get.start.input.regions
Aliases: get.start.input.regions
Keywords: internal
Description: get.start.input.regions
URL: ../../../library/SIM/html/get.start.input.regions.html

Entry: heatmap.with.clac.plot
Aliases: heatmap.with.clac.plot
Keywords: internal
Description: heatmap.with.clac.plot
URL: ../../../library/SIM/html/heatmap.with.clac.plot.html

Entry: heatmap.with.plot
Aliases: heatmap.with.plot
Keywords: internal
Description: heatmap.with.plot
URL: ../../../library/SIM/html/heatmap.with.plot.html

Entry: impute.nas.by.surrounding
Aliases: impute.nas.by.surrounding
Keywords: misc
Description: Impute NA's in array-CGH data
URL: ../../../library/SIM/html/impute.nas.by.surrounding.html

Entry: integrated.analysis
Aliases: integrated.analysis
Keywords: misc
Description: Integrated analysis of expression and copy number microarray data
URL: ../../../library/SIM/html/integrated.analysis.html

Entry: link.metadata
Aliases: link.metadata
Keywords: misc
Description: Link a metadata annotation file to expression ID
URL: ../../../library/SIM/html/link.metadata.html

Entry: make.Normal.data
Aliases: make.Normal.data
Keywords: internal
Description: Function to generate normal data for CLAC
URL: ../../../library/SIM/html/make.Normal.data.html

Entry: quantsmooth.heatmap
Aliases: quantsmooth.heatmap
Keywords: internal
Description: Function to plot smoothed copy number data along side association heatmap
URL: ../../../library/SIM/html/quantsmooth.heatmap.html

Entry: run.ia
Aliases: run.ia
Keywords: internal
Description: function to do ...
URL: ../../../library/SIM/html/run.ia.html

Entry: samples
Aliases: samples
Keywords: datasets
Description: Samples for example data
URL: ../../../library/SIM/html/samples.html

Entry: sim.plot.adj.pvals
Aliases: sim.plot.adj.pvals
Keywords: internal
Description: sim.plot.adj.pvals
URL: ../../../library/SIM/html/sim.plot.adj.pvals.html

Entry: sim.plot.pvals.on.genome
Aliases: sim.plot.pvals.on.genome
Keywords: misc
Description: Plot the p-values in whole genome overview
URL: ../../../library/SIM/html/sim.plot.pvals.on.genome.html

Entry: sim.plot.pvals.on.region
Aliases: sim.plot.pvals.on.region
Keywords: misc
Description: P-value histograms and p-values along the genome per region
URL: ../../../library/SIM/html/sim.plot.pvals.on.region.html

Entry: sim.plot.zscore.heatmap
Aliases: sim.plot.zscore.heatmap
Keywords: misc
Description: Association heatmap from z-scores
URL: ../../../library/SIM/html/sim.plot.zscore.heatmap.html

Entry: sim.update.chrom.table
Aliases: sim.update.chrom.table
Keywords: internal
Description: sim.update.chrom.table
URL: ../../../library/SIM/html/sim.update.chrom.table.html

Entry: tabulate.pvals
Aliases: tabulate.pvals
Keywords: misc
Description: Sums significant p-values for the analyzed regions
URL: ../../../library/SIM/html/tabulate.pvals.html

Entry: tabulate.top.dep.features
Aliases: tabulate.top.dep.features
Keywords: misc
Description: Lists the p-values for the dependent features
URL: ../../../library/SIM/html/tabulate.top.dep.features.html

Entry: tabulate.top.indep.features
Aliases: tabulate.top.indep.features
Keywords: misc
Description: Lists the mean z-scores for the independent features
URL: ../../../library/SIM/html/tabulate.top.indep.features.html

Entry: writeln
Aliases: writeln
Keywords: internal
Description: writeln
URL: ../../../library/SIM/html/writeln.html
