R: Integrated Analysis on two human genomic datasets

# Integrated Analysis on two human genomic datasets

## Documentation for package ‘SIM’ version 1.83.0

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

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