getDifferences

object

Reference condition to be used for testing.

referenceCondition

Defines if the distance dependency should be used to
estimate normalizationFactors. Default is <code>TRUE</code>.

fitNormFactors


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


FourCSeq is an R package dedicated to the analysis of
(multiplexed) 4C sequencing data. The package provides a
pipeline to detect specific interactions between DNA elements
and identify differential interactions between conditions. The
statistical analysis in R starts with individual bam files for
each sample as inputs. To obtain these files, the package
contains a python script (extdata/python/demultiplex.py) to
demultiplex libraries and trim off primer sequences. With a
standard alignment software the required bam files can be then
be generated.

Felix A Klein

FourCSeq

Package analyse 4C sequencing data

getDifferences function

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

getDifferences: Detect differences

Description

Usage

Arguments

Value

See Also

Examples