| methylPipe-package | Analysis of base-pair resolution DNA methylation data. |
| $,BSdataSet | Class "BSdataSet" |
| $,GElist | Class "GElist" |
| $-method | Class "BSdataSet" |
| $-method | Class "GElist" |
| binC | Class "GEcollection" |
| binC-method | Class "GEcollection" |
| binmC | Class "GEcollection" |
| binmC-method | Class "GEcollection" |
| binrC | Class "GEcollection" |
| binrC-method | Class "GEcollection" |
| binscore | Class "GEcollection" |
| binscore-method | Class "GEcollection" |
| binscore<- | Class "GEcollection" |
| binscore<--method | Class "GEcollection" |
| BSdata | Class "BSdata" |
| BSdata-class | Class "BSdata" |
| BSdataSet | Class "BSdataSet" |
| BSdataSet-class | Class "BSdataSet" |
| BSprepare | Preparing tabular data to be used to feed a BSdata object |
| chiCombP | Fisher's method implementation |
| chr | Class "GEcollection" |
| chr-method | Class "GEcollection" |
| consolidateDMRs | Consolidating Differentially Methylated Regions (DMRs) |
| extractBinGRanges | Extract genomic ranges for a given bin |
| findDMR | Identifying Differentially Methylated Regions (DMRs) |
| findDMR,methylPipe,BSdataSet | Identifying Differentially Methylated Regions (DMRs) |
| findDMR-method | Identifying Differentially Methylated Regions (DMRs) |
| findDMR-methods | Identifying Differentially Methylated Regions (DMRs) |
| findPMDs | Identifying Partially Methylated Domains (PMDs) |
| findPMDs,methylPipe,BSdata | Identifying Partially Methylated Domains (PMDs) |
| findPMDs-method | Identifying Partially Methylated Domains (PMDs) |
| findPMDs-methods | Identifying Partially Methylated Domains (PMDs) |
| GEcollection | Class "GEcollection" |
| GEcollection-class | Class "GEcollection" |
| GElist | Class "GElist" |
| GElist-class | Class "GElist" |
| getCpos | Get genomic Cxx positons for a series of genomic regions |
| getCposChr | Get genomic Cxx positons for a series of genomic regions |
| getCposDensity | Determines the density of genomic Cxx positions for a series of genomic regions |
| length | Class "GEcollection" |
| length-method | Class "BSdataSet" |
| length-method | Class "GEcollection" |
| length-method | Class "GElist" |
| mapBSdata2GRanges | Retrieve mC calls for a GRanges set of genomic regions given a BSdata object for a sample |
| mapBSdata2GRangesBin | Retrieve mC calls for a GRanges set of genomic regions given a BSdata object for a sample |
| mCsmoothing | Smoothing and plotting methylation data |
| mCsmoothing,methylPipe,BSdata | Smoothing and plotting methylation data |
| mCsmoothing-method | Smoothing and plotting methylation data |
| mCsmoothing-methods | Smoothing and plotting methylation data |
| meth.call | Function to read methylation calls |
| methstats | Exploratory statistics of samples in BSdataSet object |
| methstats,methylPipe,BSdataSet | Exploratory statistics of samples in BSdataSet object |
| methstats-method | Exploratory statistics of samples in BSdataSet object |
| methstats-methods | Exploratory statistics of samples in BSdataSet object |
| methylPipe | Analysis of base-pair resolution DNA methylation data. |
| nbins | Class "GEcollection" |
| nbins-method | Class "GEcollection" |
| plotMeth | Plot DNA methylation together with other omics, or annotation data for a genomic region |
| 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 |
| profileDNAmetBinParallel | Profile DNA methylation data for a set of genomic regions |
| show-method | Class "BSdata" |
| show-method | Class "BSdataSet" |
| show-method | Class "GEcollection" |
| show-method | Class "GElist" |
| splitChrs | Partitioning genome in chunks, for parallel computation |
| tabixdata2GR | Convert the list returned by the function scanTabix into a GRanges |
| [-method | Class "BSdataSet" |
| [-method | Class "GElist" |
| [[-method | Class "BSdataSet" |
| [[-method | Class "GElist" |
| [[<--method | Class "BSdataSet" |
| [[<--method | Class "GElist" |