Man pages for markgene/yamatCN
Yet Another Methylation Array Toolkit Copy Number Analysis
| cal_log2_ratio | Calculate log2 ratio of observed and expected values of... |
| CNV.create_anno2 | Create Conumee annotation for CNV analysis. |
| CNV.create_anno.yamat | Create CNV annotaion with 'yamat' preset. |
| conumee_analysis | Main Conumee CNV analysis |
| conumee_backbone | CNV pipeline backbone. |
| conumee_pipe | CNV pipeline based-upon Conumee package. |
| ConumeePipe-class | Conumee CNV pipeline |
| create_dnacopy_cna | Create 'CNA' object. |
| cwob_pipe | CWOB pipeline. |
| CwobPipe-class | CwobPipe pipeline |
| detail_regions | Get detail regions: yamat |
| dnacopy_analysis | Run DNAcopy analysis. |
| dnacopy_analysis.conumee | Run DNAcopy analysis: Conumee's settings. |
| dnacopy_analysis.default | Run DNAcopy analysis: DNAcopy's default settings. |
| dnacopy_analysis.yamat | Run DNAcopy analysis: Yamat's settings. |
| get_influential_loci | Get influential (i.e. outlier) loci |
| methylcnv_pipe | MethylCNV pipeline. |
| MethylCNVPipe-class | MethylCNV pipeline |
| Pipe-class | A S4 class represent CNV pipeline. |
| preprocess | Preprocess |
| report_pipe | Report an object of pipeline classes. |
| save_pipe | Save an object of pipeline classes. |
| summarize_dnacopy_segments | Summarize 'DNAcopy' segments. |
| tune_conumee_pipe | Run Conumee pipeline with different preprocessing methods. |
| write_segments | Write segments by sample. |
