methylPipe-package {methylPipe} | R Documentation

## Analysis of base-pair resolution DNA methylation data.

### Description

Analysis of base-pair resolution DNA methylation data.

### Details

Package: | methylPipe
Type: | Package
Version: | 1.0.5
Date: | 2015-02-25
License: | GPL
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

- pool.reads : Combine reads of replicates within a group

- GElist-class : This class is a set of GEcollection objects

### Author(s)

Computational Epigenomics Unit at the Center for Genomic Sciences of IIT@SEMM, Milan, Italy

kamal.fartiyal84@gmail.com

http://genomics.iit.it/groups/computational-epigenomics.html

[Package methylPipe version 1.20.0 Index]