CpGsDemo
(Package: M3D) :
Toy data for the package - 1000 CpG regions to be tested in a GRanges object
Toy data for the package - 1000 CpG regions to be tested in a GRanges object
● Data Source:
BioConductor
● Keywords: data
● Alias: CpGsDemo
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This package identifies statistically significantly differentially methylated regions of CpGs. It uses kernel methods, sepcifically the Maxmimum Mean Discrepancy (Gretton et al. 2006), to measure differences in methylation profiles, and relates these to inter-replicate changes, whilst accounting for variation in coverage profiles.
● Data Source:
BioConductor
● Keywords: package
● Alias: M3D, M3D-package
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M3D_Para
(Package: M3D) :
Computes the components of the M3D test-statistic over all regions for all
Parallel implementation of M3D_Wrapper function. Returns the two components of the M3D test-statistic - the MMD (Gretton et al. 2006) for the full data and the coverge only data, respectively - for all regions and all samples pairs, as a matrix.
● Data Source:
BioConductor
● Keywords:
● Alias: M3D_Para
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M3D_Single
(Package: M3D) :
Computes the components of the M3D test-statistic over one region for 2
Returns the two components of the M3D test-statistic - the MMD (Gretton et al. 2006) for the full data and the coverge only data, respectively. This is not intended to be called directly by the user.
● Data Source:
BioConductor
● Keywords:
● Alias: M3D_Single
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M3D_Wrapper
(Package: M3D) :
Computes the components of the M3D test-statistic over all regions for all
Returns the two components of the M3D test-statistic - the MMD (Gretton et al. 2006) for the full data and the coverge only data, respectively - for all regions and all samples pairs, as a matrix.
● Data Source:
BioConductor
● Keywords:
● Alias: M3D_Wrapper
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MMDlistDemo
(Package: M3D) :
Toy data for the package - the output of the M3D_Wrapper function.
Toy data for the package - the output of the M3D_Wrapper function.
● Data Source:
BioConductor
● Keywords: data
● Alias: MMDlistDemo
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PDemo
(Package: M3D) :
Toy data for the package - the output of the pvals function.
Toy data for the package - the output of the pvals function.
● Data Source:
BioConductor
● Keywords: data
● Alias: PDemo
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determineGroupComps
(Package: M3D) :
Creates strings of sample pair comparisons
Takes in a vector of strings of sample names and returns strings of all the comparisons, either within a testing group or between testing groups. This is not intended to be called directly by the user.
● Data Source:
BioConductor
● Keywords:
● Alias: determineGroupComps
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findComps
(Package: M3D) :
Finds columns in the M3D test-statistic matrix
Returns the columns of the test-statistic matrix that refer to specific samples. This is not intended to be called directly by the user.
● Data Source:
BioConductor
● Keywords:
● Alias: findComps
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medianFreq
(Package: M3D) :
Finds the median
Returns the median of a list of values with corresponding frequencies. This is not intended to be called directly by the user.
● Data Source:
BioConductor
● Keywords:
● Alias: medianFreq
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