addPeaks

<code>FourC</code> object for which z-scores have been calculated.

object

Threshold on z-score that has to met by all replicates
of a condition.

zScoreThresh

Threshold on adjusted p-value that has to be met in at
least one replicated of a condition.

fdrThresh


Fragments are annotated to be a z-score peak (TRUE or FALSE) based
on z-scores and fdr values for the given fragment


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

addPeaks function

Fragments are annotated to be a z-score peak (TRUE or FALSE) based
on z-scores and fdr values for the given fragment

addPeaks: Add peaks based on z-scores and adjusted p-values

Description

Usage

Arguments

Value