R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 15 found.
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RUVadj (Package: missMethyl) :

Calculate rescaled variances, empirical variances, etc. For use with RUV model fits produced using RUVfit.

● Data Source: BioConductor
● Keywords:
● Alias: RUVadj
● 0 images

RUVfit (Package: missMethyl) :

Provides an interface similar to lmFit from limma to the RUV2, RUV4, RUVinv and RUVrinv functions from the ruv package, which facilitates the removal of unwanted variation in a differential methylation analysis. A set of negative control variables, as described in the references, must be specified.

● Data Source: BioConductor
● Keywords:
● Alias: RUVfit
● 0 images

SWAN (Package: missMethyl) :

Subset-quantile Within Array Normalisation (SWAN) is a within array normalisation method for the Illumina Infinium HumanMethylation450 platform. It allows Infinium I and II type probes on a single array to be normalized together.

● Data Source: BioConductor
● Keywords:
● Alias: SWAN, SWAN.MethyLumiSet, SWAN.RGChannelSet, SWAN.default
● 0 images

contrasts.varFit (Package: missMethyl) :

Compute estimated coefficients, standard errors and LogVarRatios for a given set of contrasts.

● Data Source: BioConductor
● Keywords:
● Alias: contrasts.varFit
● 0 images

densityByProbeType (Package: missMethyl) :

Plot the overall density distribution of beta values and the density distributions of the Infinium I and II probe types.

● Data Source: BioConductor
● Keywords:
● Alias: densityByProbeType
● 1 images

getINCs (Package: missMethyl) :

Extracts the intensity data for the 613 Illumina negative controls found on 450k arrays and returns a matrix of M-values (log2 ratio of the green to red intensities).

● Data Source: BioConductor
● Keywords:
● Alias: getINCs
● 0 images

getLeveneResiduals (Package: missMethyl) :

Obtain absolute or squared Levene residuals for each CpG given a series of methylation arrays

● Data Source: BioConductor
● Keywords:
● Alias: getLeveneResiduals
● 1 images

getMappedEntrezIDs (Package: missMethyl) :

Given a set of CpG probe names and optionally all the CpG sites tested, this function outputs a list containing the mapped Entrez Gene IDs as well as the numbers of probes per gene, and a vector indicating significance.

● Data Source: BioConductor
● Keywords:
● Alias: getMappedEntrezIDs
● 0 images

gometh (Package: missMethyl) :

Tests gene ontology enrichment for significant CpGs from Illumina's Infinium HumanMethylation450 array, taking into account the differing number of probes per gene present on the array.

● Data Source: BioConductor
● Keywords:
● Alias: gometh
● 1 images

gsameth (Package: missMethyl) :

Given a user specified list of gene sets to test, gsameth tests whether significantly differentially methylated CpG sites are enriched in these gene sets.

● Data Source: BioConductor
● Keywords:
● Alias: gsameth
● 1 images