Man pages for SomatiCA
SomatiCA: identifying, characterizing, and quantifying somatic copy number aberrations from cancer genome sequencing
| admixtureRate | Estimate the admixture rate of normal cells in a tumor... |
| collapse | Collapse measurements with a certain bin size. |
| copynumberCorrected | Somatic copy number corrected by admixture rate. |
| denoise | Smoothing procedure by replacing outliers. |
| GCbiasRemoval | Correct GC bias for read depth ratio of each site. |
| GCcontent | GC content for hg19 human genome at each 1Mb interval. |
| GCcount | Calculate the GC content of given window size for a... |
| larsCBSsegment | Segmentation based on Circular Binary Segmentation followed... |
| MergeSegment | Merge neighboring segments with same somatic copy number and... |
| plotSegment | Plot segmentation. |
| plotSubclonality | Plot clonality and somatic copy number. |
| refineSegment | Refine the segmentation based on estimated somatic ratio. |
| segmentGCbiasRemoval | Correct GC bias for read depth ratio of each segment. |
| segwithratio | Segments with somatic ratio. |
| SomatiCAFormat-methods | ~~ Methods for Function 'SomatiCAFormat' in Package... |
| SomatiCA-package | Identifying, characterizing and quantifying somatic copy... |
| SomatiCApipe | SomatiCA pipeline. |
| SomatiCAUsersGuide | View SomatiCA User's Guide |
| somaticRatio | Estimate somatic ratio for given segments. |
| subclonality | Estimate subclonality for each somatic copy number... |
