CNVrd2 (version 1.10.2)

countReadInWindow: Obtain read counts in constant windows.

Description

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).

Usage

countReadInWindow(Object, ...)

Arguments

Object

An object of class CNVrd2.

...

Further aguments.

Value

readCountMatrix: a matrix of read counts for all samples (rows).

References

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.

Examples

## 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)