getMethFreqGR: Get methylation frequency genomic ranges
In jsemple19/methMatrix: Manipulate Lists of Methylation Matrices
getMethFreqGR R Documentation
Get methylation frequency genomic ranges
Description
Takes MethylDackel methylation call bedgraph files for CpG CHH and CHG motifs and creates genomic ranges for CG, GC and all other Cs. Output is a list of these three genomic ranges objects.
Usage
getMethFreqGR(baseFileName, pathToMethCalls, motifFile, minDepth = 5)
Arguments
baseFileName
base file name used in MethylDackel extract command (assumes _CpG.bedgraph, _CHH.bedgraph and _CHG.bedgraph extensions were later added by MethylDackel)
pathToMethCalls
Path to folder in which MethylDackel output is found
motifFile
Path to GRanges object with all unique CG/GC/GCGorCGC motifs in genome
minDepth
Minimum read depth. Positions with fewer than this number are discarded (default=5)
Value
Named list with CG, GC and C genomic ranges with metadata about methylation.
jsemple19/methMatrix documentation built on Aug. 19, 2022, 3:57 p.m.
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| getMethFreqGR | R Documentation |
Get methylation frequency genomic ranges
Description
Takes MethylDackel methylation call bedgraph files for CpG CHH and CHG motifs and creates genomic ranges for CG, GC and all other Cs. Output is a list of these three genomic ranges objects.
Usage
getMethFreqGR(baseFileName, pathToMethCalls, motifFile, minDepth = 5)
Arguments
baseFileName |
base file name used in MethylDackel extract command (assumes _CpG.bedgraph, _CHH.bedgraph and _CHG.bedgraph extensions were later added by MethylDackel) |
pathToMethCalls |
Path to folder in which MethylDackel output is found |
motifFile |
Path to GRanges object with all unique CG/GC/GCGorCGC motifs in genome |
minDepth |
Minimum read depth. Positions with fewer than this number are discarded (default=5) |
Value
Named list with CG, GC and C genomic ranges with metadata about methylation.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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