Integrated Analysis of gene expression and copynumber data


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Documentation for package ‘SIM’ version 1.10.0

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SIM-package Statistical Integration of Microarrays
acgh.data Array-comparative genomic hybridization data example
assemble.data Assemble the data to run the integrated analysis
chrom.table Table with chromosome arm positions
expr.data Expression data example
impute.nas.by.surrounding Impute NA's in array-CGH data
integrated.analysis Integrated analysis of expression and copy number microarray data
link.metadata Link a metadata annotation file to expression ID
RESOURCERER.annotation.to.ID Link RESOURCERER annotation file to expression ID
samples Samples for example data
SIM Statistical Integration of Microarrays
sim.plot.pvals.on.genome Plot the p-values in whole genome overview
sim.plot.pvals.on.region P-value histograms and p-values along the genome per region
sim.plot.zscore.heatmap Association heatmap from z-scores
tabulate.pvals Sums significant p-values for the analyzed regions
tabulate.top.dep.features Lists the p-values for the dependent features
tabulate.top.indep.features Lists the mean z-scores for the independent features