smoothHitPerCent

object

binWidth

Single integer defining the threshold for calling a fragment a hit.

thresh


Counts are transformed to a hit if they exceed the given threshold.
Hits are then smoothed using the number of fragments provided by binWidth.
binWidth has to be an odd number so that an equal number of fragments
to each side of the current fragment are used for smoothing.


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

smoothHitPerCent function

Counts are transformed to a hit if they exceed the given threshold.
Hits are then smoothed using the number of fragments provided by binWidth.
binWidth has to be an odd number so that an equal number of fragments
to each side of the current fragment are used for smoothing.

smoothHitPerCent: Smooth the hits of neighboring fragments

Description

Usage

Arguments

Value

See Also

Examples