Man pages for jsemple19/methMatrix
Manipulate Lists of Methylation Matrices
| allNAs | Check if vector is only NAs |
| changeAnchorCoord | Change the anchor coordinate |
| combineCGandGCmatrices | Combine CG and GC methylation matrices |
| combineCGGCgr | Convert Genomic ranges list to single genomic range with... |
| convertGRtoRelCoord | Convert Genomic Ranges to relative cooridnates |
| convertRelCoordtoGR | Convert relative cooridnates to absolute genomic position |
| fiberseqBedToBigwig | Convert fiberseq bed file to bigwig |
| fiberseqBedToMatrix | Convert fiberseq bed file to bigwig |
| getAllSampleMetaMethFreq | get average methylation frequency from all matrices |
| getFullMatrices | Get full matrix of all positions in a window even if no C |
| getMatrixLog | Read in an existing matrixLog, or create a new one |
| getMetaMethFreq | Calculate methylation frequency at each position for metagene... |
| getMethFreqGR | Get methylation frequency genomic ranges |
| getReadMatrix | Extract methylation matrix from alignment file |
| getRelativeCoord | Convert C position numbering from genomic to relative... |
| getRelativeCoordMats | Convert C position numbering from genomic to relative... |
| getSingleMoleculeMatrices | Extract list of methylation matrices |
| grlToDf | Convert Genomic ranges list to long data frame for plotting |
| makeATgrObj | Make GRanges object of all As and Ts in genome |
| makeCGorGCbed | Create bed file of CpG or GpC motifs |
| makeDirs | Make directories |
| matToGR | Convert methylation matrix to genomic ranges |
| mergeSampleMats | Merge tables listing methylation matrices for different... |
| methMats | Methylation matrix from dSMF analysis |
| parseMatchString | Clean up match string from pileup file |
| pileupToConversionStatus | Extract methylation calls from single line of pileup file |
| plotAllMatrices | Plot a list of list of single molecule matrices |
| plotDSMFmetageneDF | Plot metagene by sample |
| plotSingleMolecules | Single molecule plot of a methylation matrix |
| plotSingleMoleculesWithAvr | Single molecule plot of a methylation matrix with average... |
| poorBisulfiteConversion | Find bisulfite conversion rate of Cs in non-methylated... |
| reexports | import dopar function |
| TSS | Genomic Ranges for methMats data TSS |
