Base resolution DNA methylation data analysis


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Documentation for package ‘methylPipe’ version 1.41.0

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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"