getSkOnly {Chicago} | R Documentation

## Get S_k factors from multiple replicates

### Description

Finds s_k scaling factors for a (potentially large) number of samples. Typically, these factors are used as library size factors in some sort of differential count algorithm (DESeq, EdgeR, baySeq, ...) to find differential binding events between samples.

### Usage

    getSkOnly(files, cd)

### Arguments

`files` | Character vector containing the locations of the .chinput files to read in.
`cd` | A blank `chicagoData` object for reference, usually created with `setExperiment`.

### Value

Numeric vector of s_k factors.

### Author(s)

Jonathan Cairns, Paula Freire Pritchett, Mikhail Spivakov

### See Also

readAndMerge

### Examples

    filesDir <- file.path(system.file("extdata", package="Chicago"), "unitTestData")
    files <- file.path(filesDir, dir(filesDir))
    print(files) ##we will read in and merge these files

    designDir <- file.path(system.file("extdata", package="Chicago"), "unitTestDesign")

    cd <- setExperiment(designDir=designDir)
    s_k <- getSkOnly(files, cd)

[Package Chicago version 1.14.0 Index]