R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 40 found.
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CVplot (Package: tRanslatome) : CVplotDEGsHelpfile

The CV plot displays the coefficients of variation of the genes on the x-axis and the log2 fold changes on the y-axis. The upper plot represents a CV plot for the first level of gene expression analysis, whereas the other one refers to the second level. DEGs are color labeled. This function takes as input an object of class DEGs.

● Data Source: BioConductor
● Keywords: CV, DEGs, coefficient of variation
● Alias: CVplot
● 1 images

DEGs-class (Package: tRanslatome) : Class code{DEGs

A class generated from the function computeDEGs() containing the result of the differential expression analysis at the two expression levels.

● Data Source: BioConductor
● Keywords: DEGs, classes, differential expression
● Alias: CVplot,DEGs-method, DEGs-class, DEGs.table,DEGs-method, FC.threshold,DEGs-method, GOEnrichment,DEGs-method, Histogram,DEGs-method, MAplot,DEGs-method, RegulatoryEnrichment,DEGs-method, SDplot,DEGs-method, Scatterplot,DEGs-method, getDEGsMethod,DEGs-method, label.condition,DEGs-method, label.level.DEGs,DEGs-method, show,DEGs-method, significance.threshold,DEGs-method
● 0 images

DEGs.table (Package: tRanslatome) : DEGsTableDEGsHelpfile

This function displays an object of class numeric specifying the significance threshold used to detect DEGs. It takes as input an object of class DEGs.

● Data Source: BioConductor
● Keywords: DEGs, DEGs.table
● Alias: DEGs.table
● 0 images

EnrichedSets-class (Package: tRanslatome) : Class code{EnrichedSets

A class generated from the function RegulatoryEnrichment() containing the overrepresented post-transcriptional regulatory factors (RBPs, miRNAs, etc) from the lists of differentially expressed genes coming from the analysis of two different expression levels.

● Data Source: BioConductor
● Keywords: GO, classes, enrichment analysis
● Alias: EnrichedSets-class, Heatmap,EnrichedSets-method, Radar,EnrichedSets-method, enriched.table,EnrichedSets-method, label.level.enriched,EnrichedSets-method, show,EnrichedSets-method
● 0 images

FC.threshold (Package: tRanslatome) : FCThresholdDEGsHelpfile

This function displays an object of class numeric specifying the significance threshold used to detect DEGs. It takes as input an object of class DEGs.

● Data Source: BioConductor
● Keywords: DEGs, FC.threshold
● Alias: FC.threshold
● 0 images

GOComparison (Package: tRanslatome) : GOComparisonHelpfile

GOComparison is a function which takes as input an object of class GOsets, containing the results of a GO enrichment analysis applied to both levels, and returns an object of class GOsims, containing a variety of comparisons among the enriched GO terms.

● Data Source: BioConductor
● Keywords: DEGs, Fisher test, GO, enrichment analysis
● Alias: GOComparison
● 0 images

GOEnrichment (Package: tRanslatome) : GOEnrichmentHelpfile

GOEnrichment is a function which, given as input an object of class DEGs, identifies overrepresented GO terms among differentially expressed genes. The analysis can be applied to all the GO ontologies or restricted to GO terms specifically belonging to one ontology: molecular function, cellular component or biological process. Moreover the function can identify enriched GO terms for separate classes of genes of interest: only up-regulated genes, only down-regulated genes or both of them together. The output of the function is an object of class GOsets, containing the results of the enrichment analysis.

● Data Source: BioConductor
● Keywords: DEGs, GO, enrichment analysis
● Alias: GOEnrichment
● 0 images

GOsets-class (Package: tRanslatome) : Class code{GOsets

A class generated from the function GOEnrichment() containing the overrepresented Gene Ontology terms from the lists of differentially expressed genes coming from the analysis of two different expression levels.

● Data Source: BioConductor
● Keywords: GO, classes, enrichment analysis
● Alias: GOComparison,GOsets-method, GOsets-class, Heatmap,GOsets-method, Radar,GOsets-method, show,GOsets-method
● 0 images

GOsims-class (Package: tRanslatome) : Class code{GOsims

A class generated from the function GOComparison() containing the result of the differential expression analysis at the two expression levels.

● Data Source: BioConductor
● Keywords: GO, classes, enrichment analysis
● Alias: GOsims-class, IdentityPlot,GOsims-method, SimilarityPlot,GOsims-method, average.similarity.scores,GOsims-method, identity.matrix,GOsims-method, similarity.matrix,GOsims-method
● 0 images

Heatmap (Package: tRanslatome) : HeatmapEnrichedHelpfile

Heatmap is a function that plots the top enriched regulatory element or GO terms for the first and second level of analysis in a heatmap. The number of terms to be displayed can be set.

● Data Source: BioConductor
● Keywords: DEGs, GO, Regulatory, enrichment analysis, heatmap
● Alias: Heatmap
● 1 images