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Function to calculate the mutual information of 2 random variables, or between all pairs of rows of a numerical matrix.
● Data Source:
BioConductor
● Keywords: methods
● Alias: MI
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activeMod
(Package: maigesPack) :
Functional classification of gene groups
This function calculate profiles of expression for groups of genes in each sample of the dataset and for each biological condition (group of samples).
● Data Source:
BioConductor
● Keywords: methods
● Alias: activeMod
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This function takes an object of class maigesActMod, that is generated using the function activeMod to do functional classification of gene groups, and save an HTML file with global score for genes separated by gene groups (modules).
● Data Source:
BioConductor
● Keywords: methods
● Alias: activeModScoreHTML
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activeNet
(Package: maigesPack) :
Functional classification of gene networks
This function calculate a statistic for each gene network in each biological condition that measure the profile of activation of the network in that condition. Also the function measures the significance of the results.
● Data Source:
BioConductor
● Keywords: methods
● Alias: activeNet
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This function takes an object of class maigesActNet, that is generated using the function activeNet to do functional classification of gene groups, and save an HTML file with global score for genes separated by gene groups (modules).
● Data Source:
BioConductor
● Keywords: methods
● Alias: activeNetScoreHTML
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This function read a directory and read files containing the genes for specific gene groups. This files must have one gene per line. This function stores the gene groups read in the slot GeneGrps into objects of class maigesPreRaw.
● Data Source:
BioConductor
● Keywords: methods
● Alias: addGeneGrps
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This function read a directory and read files containing the gene pathways in TGF format. This format must have the genes of the pathway sequentially in lines numbered from 1, followed by a '#' character that separate the nodes (given by genes) from edges, that must be specified as number of the origin gene followed by a space, the number of the final gene, another space and the weight of the iteration. This function stores the gene networks read in the slot Paths into objects of class maigesPreRaw.
● Data Source:
BioConductor
● Keywords: methods
● Alias: addPaths
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This function takes a numerical matrix (or two vectors) and calculates bootstrapped (by permutation) p-values to test if the correlation value is equal to zero. If the first argument is a matrix, the p-values are calculated between all pairs of rows of the matrix.
● Data Source:
BioConductor
● Keywords: methods
● Alias: bootstrapCor
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This function takes a numerical matrix (or two vectors) and calculates bootstrapped (by permutation) p-values to test if the mutual information value is equal to zero. If the first argument is a matrix, the p-values are calculated between all pairs of rows of the matrix.
● Data Source:
BioConductor
● Keywords: methods
● Alias: bootstrapMI
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This function takes a numerical matrix and column indexes for two groups to calculate bootstrapped (by re-sampling) p-values comparing the equality of means from the two groups.
● Data Source:
BioConductor
● Keywords: methods
● Alias: bootstrapT
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