buildMACAT
(Package: macat) :
Create MACAT list from objects in workspace
This is a wrapper around the preprocessedLoader function. Use it, when you want to build a MACAT-list structure from objects already in your workspace.
● Data Source:
BioConductor
● Keywords: manip
● Alias: buildMACAT
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compute.sliding
(Package: macat) :
Compute and plot smoothing of expression values or scores along the chromosome
'compute.sliding' computes a smoothing of the expression data or scores along the chromosome using the specified kernel function. This function is also used within the 'evalScoring' function. 'plotSliding' creates a plot of the smoothed expression values / scores.
● Data Source:
BioConductor
● Keywords: manip
● Alias: compute.sliding, plotSliding
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1 images
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discreteKernelize
(Package: macat) :
Discretize and smooth expression values
returns discretized kernelized expression values and saves them to a file if argument 'saveToFile' is TRUE. For details on discretization see discretize.
● Data Source:
BioConductor
● Keywords: manip
● Alias: discreteKernelize
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discretize
(Package: macat) :
Discretize expression values
'discretize' returns the discretized expression data for all chromosomes in chrom and all samples that have a label listed in label. Discretization is performed by comparing the value gene-wise (location-wise) with the symmetric upper and lower quantile given by margin (in percent margin/2 lower and upper quantile).
● Data Source:
BioConductor
● Keywords: manip
● Alias: discretize, discretizeChromosome, discretizeOne
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discretizeAll
(Package: macat) :
Discretize complete expression matrix
perform discretization on all chromosomes and write python flat files
● Data Source:
BioConductor
● Keywords: internal
● Alias: discretizeAll
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discretize.tscores returns a discretized version of the scores in the MACATevalScoring object. Discretization is performed by comparing the value gene-wise (location-wise) with the symmetric upper and lower quantile given by margin (in percent margin/2 lower and upper quantile). discretizeAllClasses produces a flatfile readable by PYTHON.
● Data Source:
BioConductor
● Keywords: manip
● Alias: discretize.tscores, discretizeAllClasses.tscores
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evalScoring
(Package: macat) :
Score differential expression, assess significance,
This function computes for all genes on one chromosome the regularized t-statistic to score differential gene expression for two given groups of samples. Additionally these scores are computed for a number of permutations to assess significance. Afterwards these scores are smoothed with a given kernel along the chromosome to give scores for chromosomal regions.
● Data Source:
BioConductor
● Keywords: manip
● Alias: evalScoring
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evaluateParameters
(Package: macat) :
Evaluate Performance of Kernel Parameters by Cross-validation
For a given data set, chromosome, class, and kernel function, this function helps in determining optimal settings for the kernel parameter(s). The performance of individual parameter setting is assessed by cross- validation.
● Data Source:
BioConductor
● Keywords: manip
● Alias: evaluateParameters, plot.MACATevP
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1 images
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getResults
(Package: macat) :
Access results of 'evalScoring'
This function processes the result of the evalScoring function and returns a list of probe sets within chromosome regions deemed significant by MACAT. Additional annotation for these probe sets is provided along with their identifiers.
● Data Source:
BioConductor
● Keywords: manip
● Alias: getResults
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html
(Package: macat) :
HTML functions for MACAT.
HTML functions for internal usage by other MACAT functions. Normally not called by user.
● Data Source:
BioConductor
● Keywords: internal
● Alias: getHtml, myhtml
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