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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
1.42.0
1.40.0
1.38.0
1.36.0
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Version
1.42.0
License
GPL (>= 2)
Maintainer
Renee X de Menezes
Last Published
January 1st, 1970
Functions in SIM (1.42.0)
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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.