Integrated Analysis on two human genomic datasets


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Documentation for package ‘SIM’ version 1.16.0

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SIM-package Statistical Integration of Microarrays
acgh.data Array Comparative Genomic Hybridization data
assemble.data Assemble the data to run the integrated analysis
chrom.table Table with chromosome information
expr.data Expression data example
getoverlappingregions Get the overlapping regions between independent and dependent regions
impute.nas.by.surrounding Impute NA's in array-CGH data
integrated.analysis Integrated analysis of dependent and independent 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.overlapping.indep.dep.features P-value plot and mean-zscore plots with indication of overlapping features.
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.zoom.in Zoom in on heatmap
sim.plot.zscore.heatmap Association heatmap from z-scores
sim.update.chrom.table Update the chromomosome table
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