Integrated Analysis on two human genomic datasets

Documentation for package ‘SIM’ version 1.20.0

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 indepedent 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