countReadInWindow: Obtain read counts in constant windows.

In CNVrd2: CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.

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).

Author(s)

Hoang Tan Nguyen, Tony R Merriman and MA Black. [e-mail]

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)

CNVrd2 documentation built on Nov. 8, 2020, 5:30 p.m.