countReadInWindow {CNVrd2} | R Documentation |
Counting, transfering and standardizing read counts for all windows of samples. If correctGC = TRUE then all read-count windows will be corrected by the method of Yoon et al. (2009).
countReadInWindow(Object, ...)
Object |
An object of class CNVrd2. |
... |
Further aguments. |
readCountMatrix
: a matrix of read counts for all samples (rows).
Hoang Tan Nguyen, Tony R Merriman and MA Black. hoangtannguyenvn@gmail.com
Yoon, S., Xuan, Z., Makarov, V., Ye, K., Sebat, J., 2009. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome research 19 (9), 1586-1592.
## Not run: data(fcgr3bMXL) bamFiles <- dir("Bam", pattern = ".bam$") objectCNVrd2 <- new("CNVrd2", windows = 1000, chr = "chr1", st = 161100001, en = 162100000, dirBamFile = "Bam", genes = c(161592986, 161601753), geneNames = "3B") readCountMatrix <- countReadInWindow(Object = objectCNVrd2, correctGC = TRUE) readCountMatrix[1:3, 1:3] ## End(Not run)