SomatiCA-package |
Identifying, characterizing and quantifying somatic copy number aberrations from cancer genome sequencing |
admixtureRate |
Estimate the admixture rate of normal cells in a tumor sample. |
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 chromosome. |
larsCBSsegment |
Segmentation based on Circular Binary Segmentation followed by a model selection procedure on detected change points. |
MergeSegment |
Merge neighboring segments with same somatic copy number and events. |
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. |
SomatiCA |
Identifying, characterizing and quantifying somatic copy number aberrations from cancer genome sequencing |
SomatiCAFormat |
~~ Methods for Function 'SomatiCAFormat' in Package 'SomatiCA' ~~ |
SomatiCAFormat-method |
~~ Methods for Function 'SomatiCAFormat' in Package 'SomatiCA' ~~ |
SomatiCAFormat-methods |
~~ Methods for Function 'SomatiCAFormat' in Package 'SomatiCA' ~~ |
SomatiCApipe |
SomatiCA pipeline. |
SomatiCAUsersGuide |
View SomatiCA User's Guide |
somaticRatio |
Estimate somatic ratio for given segments. |
subclonality |
Estimate subclonality for each somatic copy number abberation. |