Man pages for epiG
DNA methylation and SNP calling for bisulfite sequencing data
| chain.info | chain.info |
| chain.info.epiG | chain.info |
| compute_chunk_positions | Compute chunk positions |
| coverage | coverage |
| coverage.epiG | coverage |
| create_bisulfite_model | create_bisulfite_model |
| create_error_distributions | create_error_distributions |
| create_genotype_prior_alt | create_genotype_prior_alt |
| create_genotype_prior_ref | create_genotype_prior |
| end | end position |
| end.epiG | end |
| epiG | Fit an epiG model |
| epiG.algorithm.config | Create a epiG configuration |
| epiG.chunks | epiG.chunks |
| exp_decay | exp_decay |
| fetch_alt | fetch_alt |
| fetch.reads | fetch_reads |
| fetch_reads_info | fetch_reads_info |
| fetch_ref | fetch_ref |
| genotype | genotype |
| genotype.epiG | genotype codeing C = 1, G = 2, A = 3, T = 4 |
| length.epiG | Length of model in base pairs |
| locate.DGCH | locate DGCH positions |
| locate.GCH | locate GCH positions |
| locate.HCGD | locate HCGD positions |
| locate.SNP | locate SNP positions |
| methylation | methylation |
| methylation.epiG | methylation |
| nchain | Number of chains |
| nchain.epiG | Number of chains |
| nchunks | Number of chunks |
| nchunks.epiG | Number of chunks |
| nread | Number of reads in model |
| nread.epiG | Number of reads in model |
| position.info | position.info |
| position.info.epiG | position.info |
| print.epiG | |
| print.epiG.config | print config |
| read.fasta | Read fasta |
| read.info | read.info |
| read.info.epiG | read.info |
| start | start position |
| start.epiG | start |
| strand | strand |
| strand.epiG | strand |
| subregion | subregion |
| subregion.epiG | subregion |
| symbols | symbols |
| vector.search | vector search |
