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This class adds statistical information to the exprs of the ExpressionSet as well as descriptive information to the pData of the ExpressionSet
● Data Source:
BioConductor
● Keywords: classes
● Alias: ExpressionSetWithComputation-class
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a4palette
(Package: a4Base) :
Utility function that defines a color palette for use in a4
Utility function that defines a color palette for use in a4.
● Data Source:
BioConductor
● Keywords: dplot
● Alias: a4palette
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addQuantilesColors
(Package: a4Base) :
Compute quantiles for plotGeneDE function
Compute quantiles on mean expression level for plotGeneDE function. Colors of bars in the plot could then be allocated using buckets defined by those quantiles.
● Data Source:
BioConductor
● Keywords: manip
● Alias: addQuantilesColors
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boxPlot
(Package: a4Base) :
Create a boxplot for a given gene.
Create a boxplot for a given gene. The boxplot displays the expression values (y-axis) by groupss (x-axis). The raw data are superimposed as dots, jittered for readability of the plot. Optionally, the dots can be colored by another variable.
● Data Source:
BioConductor
● Keywords:
● Alias: boxPlot
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Merge two ExpressionSet objects, checking their attributes.
● Data Source:
BioConductor
● Keywords: data
● Alias: combineTwoExpressionSet
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computeLogRatio
(Package: a4Base) :
Summary statistics for gene expression
Compute summary statistics per gene of expression data in a ExpressionSet object.
● Data Source:
BioConductor
● Keywords: data, dplot, manip
● Alias: computeLogRatio
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createExpressionSet
(Package: a4Base) :
combine gene expression and phenotype data onto a ExpressionSet object
Basically a wrapper for new('ExpressionSet',...), this function gathers gene expression and phenotype data, after having checked their compatibility.
● Data Source:
BioConductor
● Keywords: data
● Alias: createExpressionSet
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filterVarInt
(Package: a4Base) :
Filter Features On Intensity and Variance
Function to filter on intensity and variance as typically used in gene expression studies
● Data Source:
BioConductor
● Keywords: manip
● Alias: filterVarInt
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Grid version of heatmap function adapted to expressionSet objects with some specific requirements such as the possibility to display subgroups, define colors, adapt text graphical parameters (sizes...).
● Data Source:
BioConductor
● Keywords: plot
● Alias: heatmap.expressionSet
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histPvalue
(Package: a4Base) :
Plot the Distribution of P Values
This function displays the distribution of the p values using a histogram; the horizontal line represents a uniform distribution based on the p value distribution between 0.5 and 1. This represents the hypothetical p value distribution arising just by chance. This uniform distribution is used to estimate the proportion of differentially expressed genes.
● Data Source:
BioConductor
● Keywords: dplot
● Alias: histPvalue, histPvalue,MArrayLM-method, histPvalue,limma-method, histPvalue,numeric-method, histPvalue,tTest-method
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