copa
(Package: copa) :
Calculate COPA Scores from a Set of Microarrays
This function calculates COPA scores from a set of microarrays. Input can be an ExpressionSet, or a matrix or data.frame.
● Data Source:
BioConductor
● Keywords: univar
● Alias: copa
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This package is used to compute copa scores, p-values based on permutation, and plots of paired genes.
● Data Source:
BioConductor
● Keywords: package
● Alias: copa-package
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copaFilter
(Package: copa) :
Pre-filter Genes for COPA Analysis
This function is used to pre-filter genes prior to doing a COPA analysis. The filtering is based on the nth percentile of the outlier samples for each gene. This function is an internal function and not intended to be called by the end user.
● Data Source:
BioConductor
● Keywords: internal
● Alias: copaFilter, copaFilter, ExpressionSet-method, copaFilter, data.frame-method, copaFilter, matrix-method, copaFilter-methods, do.copaFilter
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copaPerm
(Package: copa) :
Measure Significance of COPA by Permutation
This function can be used to determine the significance of the results that one gets from running copa on a particular dataset, based on permuting the class assignments.
● Data Source:
BioConductor
● Keywords: manip
● Alias: copaPerm
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tableCopa
(Package: copa) :
Summarize copa results
This function will output a table showing the number of gene pairs at each number of outliers.
● Data Source:
BioConductor
● Keywords: manip
● Alias: tableCopa
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getans
(Package: copa) :
Interactive Function
A function to query the end user. This is an internal function and not intended to be called directly by the end user.
● Data Source:
BioConductor
● Keywords: internal
● Alias: getans
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pSum
(Package: copa) :
Compute all pairwise sums
A function that computes all pairwise sums for a vector of numbers. This is an internal function and is not intended for use by end-users.
● Data Source:
BioConductor
● Keywords: internal
● Alias: pSum
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perm.mat
(Package: copa) :
Produce a Matrix of Permuted Classlabels
This function makes a matrix of permuted classlabels. This is not intended to be called directly by end users.
● Data Source:
BioConductor
● Keywords: internal
● Alias: perm.mat
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plotCopa
(Package: copa) :
Plot Gene Pairs fom the Results of Running copa
This function can be used to visualize pairs of genes that may be involved in recurrent gene fusion in cancer.
● Data Source:
BioConductor
● Keywords: hplot
● Alias: plotCopa
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scatterPlotCopa
(Package: copa) :
Create scatterplots of interesting gene pairs
This function allows one to create scatterplots of gene pairs that may be involved in recurrent gene fusion in cancer.
● Data Source:
BioConductor
● Keywords: hplot
● Alias: scatterPlotCopa
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