getSkOnly: Get S_k factors from multiple replicates

In Chicago: CHiCAGO: Capture Hi-C Analysis of Genomic Organization

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)

Chicago documentation built on Nov. 8, 2020, 8:15 p.m.