SIM: Integrated Analysis on two human genomic datasets

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Finds associations between two human genomic datasets.

Author
Renee X. de Menezes and Judith M. Boer
Date of publication
None
Maintainer
Renee X. de Menezes <r.xavierdemenezes@vumc.nl>
License
GPL (>= 2)
Version
1.44.0

View on Bioconductor

Man pages

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...
impute.nas.by.surrounding
Impute NA's in array-CGH data
integrated.analysis
Integrated analysis of dependent and indepedent microarray...
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-package
Statistical Integration of Microarrays
sim.plot.overlapping.indep.dep.features
P-value plot and mean-zscore plots with indication of...
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

Files in this package

SIM/DESCRIPTION
SIM/NAMESPACE
SIM/R
SIM/R/RESOURCERER.annotation.to.ID.R
SIM/R/assemble.data.R
SIM/R/getoverlappingregions.R
SIM/R/impute.nas.by.surrounding.R
SIM/R/integrated.analysis.R
SIM/R/link.metadata.R
SIM/R/run.ia.R
SIM/R/sim.plot.overlapping.indep.dep.features.R
SIM/R/sim.plot.pvals.on.genome.R
SIM/R/sim.plot.pvals.on.region.R
SIM/R/sim.plot.zscore.heatmap.R
SIM/R/sim.update.chrom.table.R
SIM/R/tabulate.pvals.R
SIM/R/tabulate.top.dep.features.R
SIM/R/tabulate.top.indep.features.R
SIM/R/zzz.R
SIM/build
SIM/build/vignette.rds
SIM/data
SIM/data/acgh.data.rda
SIM/data/chrom.table.rda
SIM/data/expr.data.rda
SIM/data/samples.rda
SIM/inst
SIM/inst/CITATION
SIM/inst/doc
SIM/inst/doc/SIM.R
SIM/inst/doc/SIM.Rnw
SIM/inst/doc/SIM.pdf
SIM/man
SIM/man/RESOURCERER.annotation.to.ID.Rd
SIM/man/SIM-package.Rd
SIM/man/acgh.data.Rd
SIM/man/assemble.data.Rd
SIM/man/chrom.table.Rd
SIM/man/expr.data.Rd
SIM/man/getoverlappingregions.Rd
SIM/man/impute.nas.by.surrounding.Rd
SIM/man/integrated.analysis.Rd
SIM/man/link.metadata.Rd
SIM/man/samples.Rd
SIM/man/sim.plot.overlapping.indep.dep.features.Rd
SIM/man/sim.plot.pvals.on.genome.Rd
SIM/man/sim.plot.pvals.on.region.Rd
SIM/man/sim.plot.zoom.in.Rd
SIM/man/sim.plot.zscore.heatmap.Rd
SIM/man/sim.update.chrom.table.Rd
SIM/man/tabulate.pvals.Rd
SIM/man/tabulate.top.dep.features.Rd
SIM/man/tabulate.top.indep.features.Rd
SIM/src
SIM/src/withinWindow.c
SIM/vignettes
SIM/vignettes/SIM.Rnw
SIM/vignettes/SIM.bib