calcTNullFast
(Package: sigPathway) :
Compute Null T Distribution for Each Gene
Computes a null t distribution for each gene by permuting the phenotypes.
● Data Source:
BioConductor
● Keywords: array, htest
● Alias: calcTNullFast
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calcTStatFast
(Package: sigPathway) :
Compute T-Statistics and Corresponding P-Values
Computes t-statistics and corresponding p-values.
● Data Source:
BioConductor
● Keywords: array, htest
● Alias: calcTStatFast
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1 images
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calculate.GSEA
(Package: sigPathway) :
Calculate 2-sided statistics based on the GSEA algorithm
Calculates the 2-sided statistics based on the GSEA algorithm.
● Data Source:
BioConductor
● Keywords: array, htest
● Alias: calculate.GSEA
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0 images
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calculate.NGSk
(Package: sigPathway) :
Calculate NGSk (NTk-like) statistics with gene label permutation
Calculates the NGSk (NTk-like) statistics with gene label permutation and the corresponding p-values and q-values for each selected pathway.
● Data Source:
BioConductor
● Keywords: array, htest
● Alias: calculate.NGSk
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Calculates the NTk and NEk statistics and the corresponding p-values and q-values for each selected pathway.
● Data Source:
BioConductor
● Keywords: array, htest
● Alias: calculate.NEk, calculate.NTk
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estimateNumPerm
(Package: sigPathway) :
Compute the Number of Unique Permutations for a Phenotype Vector
Computes the number of unique permutations based on a vector of phenotypes and the number of groups.
● Data Source:
BioConductor
● Keywords: array, htest
● Alias: estimateNumPerm
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Gives the statistics for the probe sets associated with a pathway.
● Data Source:
BioConductor
● Keywords: array, htest
● Alias: getPathwayStatistics.NGSk
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getPathwayStatistics
(Package: sigPathway) :
Give the statistics for the probe sets in a pathway
Gives the statistics for the probe sets associated with a pathway.
● Data Source:
BioConductor
● Keywords: array, htest
● Alias: getPathwayStatistics
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importGeneSets
(Package: sigPathway) :
Import gene sets stored in GMT, GMX, GRP, and XML file formats
Imports gene sets stored in GMT, GMX, GRP, and XML file formats and converts them to sigPathway's preferred format.
● Data Source:
BioConductor
● Keywords: datagen, file
● Alias: gmtToG, gmxToG, grpToG, importGeneSets, xmlToG
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rankPathways.NGSk
(Package: sigPathway) :
Summarizes Top Pathways from One of the Pathway Analyses
Summarizes top pathways from one of the pathway analyses (i.e., calculate.NTk, calculate.NEk, calculate.NGSk, or calculate.GSEA)
● Data Source:
BioConductor
● Keywords: array, htest
● Alias: rankPathways.NGSk
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