R Graphical Manual

Last data update: 2014.03.03

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Classification

Results 1 - 10 of 23 found.
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BSdata-class (Package: methylPipe) : Class "BSdata"

This class is used in the methylPipe library to point to a TABIX compressed file containing base-resolution DNA-methylation data and reference genome sequence

● Data Source: BioConductor
● Keywords: classes
● Alias: BSdata, BSdata-class, show,BSdata-method
● 0 images

BSdataSet-class (Package: methylPipe) : Class "BSdataSet"

This class is used in the methylPipe library to store a set of BSdata objects

● Data Source: BioConductor
● Keywords: classes
● Alias: BSdataSet, BSdataSet-class, length,BSdataSet-method, show,BSdataSet-method
● 0 images

BSprepare (Package: methylPipe) : Preparing tabular data to be used to feed a BSdata object

Appending p-values and TABIX compressing tabular data containing DNA-methylation data so that they can be used to create a BSdata object.

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

GEcollection-class (Package: methylPipe) : Class "GEcollection"

This class is used in the methylPipe library to define and manipulate a set of genomic regions and the associated DNA methylation patterns

● Data Source: BioConductor
● Keywords: classes
● Alias: GEcollection, GEcollection-class, binC, binC,GEcollection-method, binmC, binmC,GEcollection-method, binrC, binrC,GEcollection-method, binscore, binscore,GEcollection-method, binscore<-, binscore<-,GEcollection-method, chr, chr,GEcollection-method, length, length,GEcollection-method, nbins, nbins,GEcollection-method, show,GEcollection-method
● 0 images

GElist-class (Package: methylPipe) : Class "GElist"

This class is used in the methylPipe library to collect a set of GEcollection objects

● Data Source: BioConductor
● Keywords: classes
● Alias: GElist, GElist-class, length,GElist-method, show,GElist-method
● 0 images

chiCombP (Package: methylPipe) : Fisher's method implementation

Fisher's method implementation, used to combine the results from several independent tests bearing upon the same overall hypothesis.

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

consolidateDMRs (Package: methylPipe) : Consolidating Differentially Methylated Regions (DMRs)

Joins differentially methylated regions according to their proximity to each other, statistical significance and methylation difference

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

extractBinGRanges (Package: methylPipe) : Extract genomic ranges for a given bin

For genomic ranges with N bins, extract the Genomic ranges for a given bin.

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

findDMR (Package: methylPipe) : Identifying Differentially Methylated Regions (DMRs)

Identifying differentially methylated regions for pairwise or multiple samples comparision.

● Data Source: BioConductor
● Keywords:
● Alias: findDMR, findDMR,BSdataSet-method, findDMR,methylPipe,BSdataSet, findDMR,methylPipe,BSdataSet-method, findDMR-methods
● 0 images

findPMDs (Package: methylPipe) : Identifying Partially Methylated Domains (PMDs)

This function is a wrapper function to identify partially methylated domains (PMDs) in Bis-seq data.

● Data Source: BioConductor
● Keywords:
● Alias: findPMDs, findPMDs,BSdata-method, findPMDs,methylPipe,BSdata, findPMDs,methylPipe,BSdata-method, findPMDs-methods
● 0 images