| beta_matrix | Beta value matrix |
| CancerDetector | Cancer Detector |
| CancerDetector.markers | Cancer-specific marker parameter |
| CancerDetector.reads | Fragment-level methylation state for cancer detection |
| cfDeconvolve | cfDNA methylation read deconvolution |
| cfDeconvolve.markers | Tissue-specific marker parameter |
| cfDeconvolve.reads | Fragment-level methylation state for tissue deconvolution |
| cfSort | cfSort: tissue deconvolution |
| cfSort.reads | Fragment-level methylation state for cfSort tissue deconvolution |
| cfsort_markers | cfSort markers |
| CpG_OB_demo | Methylation information for CpG on the original bottom strand (OB) |
| CpG_OT_demo | Methylation information for CpG on the original top strand (OT) |
| demo.fragment_level.meth.bed | Fragment-level methylation information |
| demo.refo_frag.bed | Fragment-level information |
| demo.refo_meth.bed | Methylation information on fragments |
| demo.sorted.bed | Paired-end sequencing reads |
| GenerateFragMeth | Generate fragment-level information about methylation states |
| GenerateMarkerParam | Generate the methylation pattern of markers |
| markers.bed | Genomic postions of markers |
| marker_index | Marker name |
| MergeCpGs | Generate fragment-level methylation states of CpGs |
| MergePEReads | Generate fragment-level information for paired-end sequencing reads |
| sample_type | Sample type |