countReadInWindow {CNVrd2} | R Documentation

## 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).

### Author(s)

Hoang Tan Nguyen, Tony R Merriman and MA Black. hoangtannguyenvn@gmail.com

### 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)

[Package CNVrd2 version 1.20.0 Index]