plotNormalizationFactors

A <code>FourC</code> object, after successfully calling <code>getZScores</code>.

object

If <code>TRUE</code> (default), the normalizationFactors are plotted as a
function for distance from the viewpoint. Otherwise they are plotted
as a function of ranks.

dist

If <code>TRUE</code>, sizeFactors are calculated and plotted as
horizontal bars.

sizeFactors


<code>plotNormalizationFactors</code> generates plots of the fits used to calculate the z-scores.


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

plotNormalizationFactors function

<code>plotNormalizationFactors</code> generates plots of the fits used to calculate the z-scores.

plotNormalizationFactors: Plot the estimated normalization factors.

Description

Usage

Arguments

Details

See Also

Examples