methylPipe-package: Analysis of base-pair resolution DNA methylation data.
Description
Analysis of base-pair resolution DNA methylation data.Details
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Package: |
| methylPipe |
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Type: |
| Package |
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Version: |
| 1.0.5 |
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Date: |
| 2015-02-25 |
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License: |
| GPL |
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Depends: |
| methods |
The package offers the following functionalities:
- BSdata-class : This class is used in to point to a TABIX compressed file containing base-resolution DNA-methylation data and reference genome sequence
- mCsmoothing : Smoothing and plotting methylation data, even chromosome wide
- findPMDs : Find partially methylated regions for a given sample
- mapBSdata2GRanges : Retrieve mC calls for a GRanges from a BSdata object for a sample
- BSdataSet-class : This class is a set of BSdata objects
- findDMR : Identifying differentially methylated regions for pairwise or multiple samples comparision
- methstats : Descriptive methylation statistics of samples within BSdataSet object
- consolidateDMRs : Joins differentially methylated regions according to their proximity to each other, statistical significance, methylation difference and DMR type
- GEcollection-class : This class is used to define and manipulate a set of genomic regions and the associated DNA methylation patterns
- getCpos : Get genomic Cxx positons for a series of genomic regions
- getCposDensity : Determines the density of genomic Cxx positions for a series of genomic regions
- profileDNAmetBin : Profile DNA methylation data for a set of genomic regions
- plotMeth : Plot the methylation/omics data of a GEcollection object
- BSprepare : Preparing tabular data to be used to feed a BSdata object
- meth.call : Reads the methylation information from the sorted SAM files generated from BISMARK aligner
- GElist-class : This class is a set of GEcollection objects