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... |
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