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MineICA (version 1.6.0)

Analysis of an ICA decomposition obtained on genomics data

Description

The goal of MineICA is to perform Independent Component Analysis (ICA) on multiple transcriptome datasets, integrating additional data (e.g molecular, clinical and pathological). This Integrative ICA helps the biological interpretation of the components by studying their association with variables (e.g sample annotations) and gene sets, and enables the comparison of components from different datasets using correlation-based graph.

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Version

Version

1.6.0

License

GPL-2

Maintainer

Anne Biton

Last Published

February 15th, 2017

Functions in MineICA (1.6.0)

Retrieve sample contributions stored in an IcaSet object as a list.

Association of a colour with each annotation level

clusterSamplesByComp_multiple

Cluster samples from an IcaSet

clusterSamplesByComp

Cluster samples from an IcaSet

Retrieve and set Source S and Mixing matrix A from IcaSet

addGenesToGoReport

Add Symbol IDs to hyperGTest results

Extract projection values

Output of hyperGtest

Runs an enrichment analysis per component using package GOstats.

Plots graph using

plotDens2classInComp_plotOnly

Plots the densities or boxplots of the component contributions using ggplot2.

runCompareIcaSets

runCompareIcaSets

compareAn2graphfile

compareAn2graphfile

Union and intersection of contributing genes

IcaSet-object containing a FastICA decomposition of gene expression microarrray-based data of bladder cancer samples.

Plots the Gaussian fitted by Mclust on several numeric vectors

IcaSet-object containing a FastICA decomposition of gene expression microarrray-based data of bladder cancer samples.

plot_heatmapsOnSel

Plot heatmap associated with each component

Enrichment analysis through GOstats

plotPosAnnotInComp

Histograms of sample contributions for each annotation level

plotPosOneAnnotInComp_ggplot

Tests if groups of samples are differently distributed on the components and do the corresponding plots.

Description of features using package biomaRt.

Write rnk files containing gene projections

writeGostatsHtmltable

Writes enrichment results in a HTML file

clusterFastICARuns

Run of fastICA and JADE algorithms

Class to contain parameters for the analysis of an ICA decomposition.

plotPosOneAnnotLevInComp_ggplot

Plots the position of a subset of samples in the histogram of all samples using ggplot2.

selectFeatures_IQR

Selection of features based on their IQR

plotPosSamplesInComp

Histograms of sample subsets

selectWitnessGenes

selectWitnessGenes

Carbayo annotation data

Annotation of features using an annotation package

clusVarAnalysis

Tests association between clusters of samples and variables

Comparison of IcaSet objects using correlation

Correlation between two matrices

IcaSet-object containing a FastICA decomposition of gene expression microarrray-based data of bladder cancer samples.

IcaSet-object containing a FastICA decomposition of gene expression microarrray-based data of bladder cancer samples.

Plots the Gaussian fitted by Mclust

Plots an histogram and Gaussian fitted by Mclust

Retrieve feature/gene projections stored in an IcaSet object as a list.

wilcoxOrKruskalOnA

Comparison of distributions of sample groups

Features annotation of an object of class IcaSet.

annotReciprocal

annotReciprocal

build_sortHeatmap

Build the heatmap matrices

This function builds an object of class IcaSet.

Retrieve and set data from IcaSet

nbOccByGeneInComp

nbOccByGeneInComp

Carbayo expression data

nbOccInComp_simple

nbOccInComp_simple

Select components the features contribute to

Generate node attributes

qualVarAnalysis

Tests association between qualitative variables and components.

quantVarAnalysis

Correlation between variables and components.

Run of fastICA and JADE algorithms

Select contributing features/genes

writeProjByComp

writeProjByComp

writeHtmlResTestsByAnnot

Tests if groups of samples are differently distributed on the components according and do the corresponding plots.

annotFeaturesWithBiomaRt

Annotation of features using biomaRt

annotFeaturesComp

Features annotation

buildMineICAParams

Creates an object of class MineICAParams

Retrieve feature and sample values on a component stored in an IcaSet object.

Runs enrichment analysis of contributing genes

Class to Contain and Describe an ICA decomposition of High-Throughput Data.

Retrieve and set component labels, indices, and witness genes from IcaSet

mergeGostatsResults

Merge enrichment results obtained for different databases into one file per component.

plotDensAllAnnotInAllComp

Tests if groups of samples are differently distributed on the components according and do the corresponding plots.

plotDensOneAnnotInAllComp

Tests if groups of samples are differently distributed on the components and do the corresponding plots.

Run analysis of an IcaSet object