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SIM (version 1.42.0)

Integrated Analysis on two human genomic datasets

Description

Finds associations between two human genomic datasets.

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Version

Version

1.42.0

License

GPL (>= 2)

Last Published

February 15th, 2017

Functions in SIM (1.42.0)

expr.data

Expression data example
link.metadata

Link a metadata annotation file to expression ID
tabulate.top.indep.features

Lists the mean z-scores for the independent features
sim.plot.overlapping.indep.dep.features

P-value plot and mean-zscore plots with indication of overlapping features.
SIMAT-package

This package is for processing GC-SIM-MS data
getTargetTable

Get target table information
assemble.data

Assemble the data to run the integrated analysis
sim.update.chrom.table

Update the chromomosome table
getPeak

Get all peaks corresponding to targets in several runs
acgh.data

Array Comparative Genomic Hybridization data
sim.plot.pvals.on.region

P-value histograms and P-values along the genome per region
getScore

Calculate similarity score for a peak
RItable

Extracted RI standard information from a csv file.
chrom.table

Table with chromosome information
integrated.analysis

Integrated analysis of dependent and indepedent microarray data
target.table

Extracted target information from a csv file.
sim.plot.pvals.on.genome

Plot the P-values in whole genome overview
tabulate.pvals

Sums significant P-values for the analyzed regions
Targets

Targets information in a list.
readMSL

Read mass spectral library (MSL) files
SIM-package

Statistical Integration of Microarrays
getoverlappingregions

Get the overlapping regions between independent and dependent regions
getRI

Generate a calibration function
tabulate.top.dep.features

Lists the P-values for the dependent features
getRIStandard

Get the RI standard information
putTargetTable

Put target table information
impute.nas.by.surrounding

Impute NA's in array-CGH data
readCDF

Read raw mass spectrometry data in netCDF files
RESOURCERER.annotation.to.ID

Link RESOURCERER annotation file to expression ID
sim.plot.zoom.in

Zoom in on heatmap
sim.plot.zscore.heatmap

Association heatmap from z-scores
Library

Extracted compound information from an MSL library.
plotTIC

Plotting TIC of one run
getPeakScore

Calculate the similarity score for all peaks
samples

Samples for example data
Run

Extracted peaks from one SIM run.
optFrag

Fragment selection through optimization
plotEIC

Plotting EIC of one peak
getTarget

Get target information
getEIC

Get the EIC of a peak
writeMSL

Write targets information into a file with mass spectral library (MSL) format.