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SIM (version 1.40.0)

Integrated Analysis on two human genomic datasets

Description

Finds associations between two human genomic datasets.

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Version

Version

1.40.0

License

GPL (>= 2)

Maintainer

Renee X de Menezes

Last Published

February 15th, 2017

Functions in SIM (1.40.0)

link.metadata

Link a metadata annotation file to expression ID
chrom.table

Table with chromosome information
integrated.analysis

Integrated analysis of dependent and indepedent microarray data
acgh.data

Array Comparative Genomic Hybridization data
impute.nas.by.surrounding

Impute NA's in array-CGH data
RESOURCERER.annotation.to.ID

Link RESOURCERER annotation file to expression ID
expr.data

Expression data example
assemble.data

Assemble the data to run the integrated analysis
samples

Samples for example data
getoverlappingregions

Get the overlapping regions between independent and dependent 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
sim.plot.pvals.on.genome

Plot the P-values in whole genome overview
sim.update.chrom.table

Update the chromomosome table
sim.plot.pvals.on.region

P-value histograms and P-values along the genome per region
tabulate.pvals

Sums significant P-values for the analyzed regions
SIM-package

Statistical Integration of Microarrays
sim.plot.overlapping.indep.dep.features

P-value plot and mean-zscore plots with indication of overlapping features.
sim.plot.zoom.in

Zoom in on heatmap
sim.plot.zscore.heatmap

Association heatmap from z-scores