distFitMonotone

Matrix of variance stabilized count data in the defined interval around
the viewpoint.

count

Data frame with all the information on restriction
fragments and the interval around the viewpoint.

fragData

Approximate number of fragments between two breaks of the B-spline
basis. <code>floor((number of fragments))/alpha)</code> is passed to <code>create.bspline.basis</code>
as <code>nbasis</code> argument (if this value is smaller than 4, 4 is the default value for <code>nbasis</code>).
Default is <code>20</code>.

alpha

Penalty term passed to  <code>fdPar</code> as <code>lambda</code> argument.
Default is <code>0.1</code>.

penalty

Defines if zero values should be removed from the fit.
Default is <code>FALSE</code>.

removeZeros


<code>distFitMonotone</code> takes the variance stabilized count values and
calculates a monotone fit for the distance dependency. The position
information about the viewpoint is stored in <code>fragData</code>.
The signal trend is fitted for the data left and right to the viewpoint
separately using the fda 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

distFitMonotone function

<code>distFitMonotone</code> takes the variance stabilized count values and
calculates a monotone fit for the distance dependency. The position
information about the viewpoint is stored in <code>fragData</code>.
The signal trend is fitted for the data left and right to the viewpoint
separately using the fda package.

distFitMonotone: Fit the distance dependency

Description

Usage

Arguments

Value