Man pages for methylPipe
Base resolution DNA methylation data analysis
| BSdata-class | Class "BSdata" |
| BSdataSet-class | Class "BSdataSet" |
| BSprepare | Preparing tabular data to be used to feed a BSdata object |
| chiCombP | Fisher's method implementation |
| consolidateDMRs | Consolidating Differentially Methylated Regions (DMRs) |
| extractBinGRanges | Extract genomic ranges for a given bin |
| findDMR | Identifying Differentially Methylated Regions (DMRs) |
| findPMDs | Identifying Partially Methylated Domains (PMDs) |
| GEcollection-class | Class "GEcollection" |
| GElist-class | Class "GElist" |
| getCpos | Get genomic Cxx positons for a series of genomic regions |
| getCposDensity | Determines the density of genomic Cxx positions for a series... |
| mapBSdata2GRanges | Retrieve mC calls for a GRanges set of genomic regions given... |
| mCsmoothing | Smoothing and plotting methylation data |
| meth.call | Function to read methylation calls |
| methstats | Exploratory statistics of samples in BSdataSet object |
| methylPipe-package | Analysis of base-pair resolution DNA methylation data. |
| plotMeth | Plot DNA methylation together with other omics, or annotation... |
| pool.reads | Function to pool reads of replicates |
| process.hmc | Processing hmC information from the MLML output |
| profileDNAmetBin | Profile DNA methylation data for a set of genomic regions |
| splitChrs | Partitioning genome in chunks, for parallel computation |
| tabixdata2GR | Convert the list returned by the function scanTabix into a... |
