plotDifferences

object

Window sizes around the viewpoint for which plots are generated.

plotWindows

diffThresh

Auxiliary <code>GRanges</code> object that contains information about the
viewpoint and closest gene TSS.

controls

Auxiliary <code>TranscriptDb</code> object that contains gene models for the
investigated organism.

txdb

Condition A and B, for which the comparison is plotted.

conditionAB


<code>plotDifferences</code> generate plots to investigate the results
of <code>getDifferences</code>


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

plotDifferences function

<code>plotDifferences</code> generate plots to investigate the results
of <code>getDifferences</code>

plotDifferences: Plot differences

Description

Usage

Arguments

See Also

Examples