segmentSamples {CNVrd2} | R Documentation |
Segment read-count windows into region having similar signal values by using the DNAcopy package (Venkatraman and Olshen, 2007) and refine this process to obtain segmentation scores at genes.
segmentSamples(Object, ...)
Object |
An object of class CNVrd2. |
... |
Optional arguments. |
segmentResults |
All results of the segmentation process. |
segmentationScores |
Segmentation scores of the gene(s) being measured. |
observedReadCountRatios |
Observed read-count ratios of genes. This value is a matrix of observed read-count ratios at genes if (only inputBamFile = TRUE). |
stdCntMatrix |
Matrix of read counts (standardized). |
Hoang Tan Nguyen, Tony R Merriman and MA Black. hoangtannguyenvn@gmail.com
Venkatraman, E., Olshen, A. B., 2007. A faster circular binary segmentation algorithm for the analysis of array chg data. Bioinformatics 23 (6), 657-663.
countReadInWindow
, DNAcopy
data(fcgr3bMXL) ## Not run: resultSegment <- segmentSamples(Object = objectCNVrd2, stdCntMatrix = readCountMatrix)