R Graphical Manual

Last data update: 2014.03.03

Data Source

R Release (3.2.3)
CranContrib
BioConductor
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Data Type

Packages
Functions
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Data set

Classification

Results 1 - 10 of 27 found.
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bgAdjust (Package: charm) :

Estimate and remove background signal using anti-genomic background probes

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

clusterMaker (Package: charm) :

Redefine array regions given chromosomal coordinates.

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

cmdsplot (Package: charm) :

Unsupervised clustering of charm data samples by classical multi-dimensional scaling.

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

controlQC (Package: charm) :

Make boxplots of the non-control probes and the control probes (after spatial and background correction but before any normalization), to confirm that the control probes have a lower distribution of intensities than the non-control probes.

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

countGC (Package: charm) :

Return the GC content for each probe

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

cpgdensity (Package: charm) :

Calculate the CpG density for a set of windows

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

dmrFdr (Package: charm) :

Estimate false discovery rate q-values for a set of differentially methylated regions (found using the dmrFinder function) using a permutation approach. For differentially methylated regions found using the dmrFind function, use the qval function instead.

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

dmrFind (Package: charm) :

Identify DMR candidates using a regression-based approach and correcting for batch effects.

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

dmrFinder (Package: charm) :

Find differentially methylated regions (DMRs) from tiling microarray data. If you want to adjust for covariates (including batch effects estimated using SVA) or if your covariate of interest is continuous, use the dmrFind function.

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

dmrPlot (Package: charm) :

Plot differentially methylated regions (DMRs) from tiling microarray data that were identified using the dmrFinder function. To plot DMRs identified using the dmrFind function, use the plotDMRs function.

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