estimateTechnicalNoise {Chicago} | R Documentation

## Estimate Technical Noise

### Description

Calculates the expected technical noise based on trans read pairs.

### Usage

    estimateTechnicalNoise(cd, plot = TRUE, outfile = NULL)

### Arguments

`cd` | A `chicagoData` object.
`plot` | Logical - if `TRUE`, then output a diagnostic plot.
`outfile` | `NULL`, or a character string. If `NULL`, the diagnostic plot is outputted to the current plotting device. If a character string, e.g. `outfile="tech.pdf"`, then the plot will be outputted to that file.

### Value

An object of class `chicagoData`, with additional columns "tlb", "tblb", "Tmean".

### Warning

The object `intData(cd)` is updated by reference. Thus, `intData(cd)` will be altered. See vignette for further information.

### Author(s)

Mikhail Spivakov, Jonathan Cairns, Paula Freire Pritchett

### See Also

`chicagoPipeline`

### Examples

    data(cdUnitTest)

    ##modifications to cdUnitTest, ensuring it uses correct design directory
    designDir <- file.path(system.file("extdata", package="Chicago"), "unitTestDesign")
    cdUnitTest <- modifySettings(cd=cdUnitTest, designDir=designDir)

    cdUnitTest <- estimateTechnicalNoise(cdUnitTest)

[Package Chicago version 1.15.0 Index]