getDifferences: Detect differences

In FourCSeq: Package analyse 4C sequencing data

Description

getDifferences detects differences in the interaction frequencies between different conditions. For each viewpoint all possible combinations of conditions are tested using the DESeq2 package.

Usage

getDifferences(object, referenceCondition = NULL, fitNormFactors = TRUE)

Arguments

object	A FourC object.
referenceCondition	Reference condition to be used for testing.
fitNormFactors	Defines if the distance dependency should be used to estimate normalizationFactors. Default is TRUE.

Value

Returns an updated FourC object that contains the results and information from the differential testing. Normalization factors are added to the assays slot.

Author(s)

Felix A. Klein, [e-mail]

See Also

FourC, getZScores, estimateDispersions, nbinomWaldTest

Examples

                       
data(fcf, package="FourCSeq")

fcf <- getDifferences(fcf, referenceCondition="WE_68h")

results <- getAllResults(fcf)
results

FourCSeq documentation built on Nov. 8, 2020, 7:08 p.m.