Man pages for BIMSBbioinfo/AmpliconBiSeq
analyzing amplicon bisulfite sequencing data
| ampData | get data from AmpliconViews object |
| AmpliconViews | Makes an AmpliconViews object |
| AmpliconViews-class | An S4 class for amplicon bisulfite sequencing |
| designPrimers | Design primers for amplicons |
| filterPrimers | filter primers based on thresholds |
| getAmplicon | subset AmpliconViews object |
| getAmpliconNames | get amplicon Names from AmpliconView object |
| getAmpliconRanges | get locations of amplicons from AmpliconViews object |
| getAvMeth | get average methylation for bases in an amplicon |
| getCoverage | get coverage for bases in an amplicon |
| getExampleMethMat | get example methylation matrix the methylation matrix of an... |
| getMetaMethylation | get meta-methylation info from AmpliconView object |
| getMethMat | get methylation matrix |
| getSampleNames | get sample Names from AmpliconViews object |
| getSimilarity | get similarity for base methylation profiles in an amplicon |
| methRatio | convert ampliconView objects to a table of methylation ratio |
| plotAmpliconView | plot ampliconView object with Gviz |
| primers2ranges | convert primer list to genomic intervals |
| show-methods | show method for methylKit classes |
| spikeCheck | check the quality of the spike-ins |
