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" |