combineFragEnds

object

Multiplication factor that can be used to multiply the
counts of fragments which only have one valid end. Default is <code>1</code>.
<code>filter</code> is automatically set to <code>TRUE</code> if <code>multFactor</code>
is different from 1.

multFactor

If filter is <code>TRUE</code>, only reads from valid fragment
ends are summed up for each fragment. This means if only one fragment end
is valid only counts from this end are considered.
If filter is <code>FALSE</code>, counts from both fragment ends are summed up
without any filtering.

filter


<code>combineFragEnds</code> combines the counts of both fragment ends. A
multiplication factor can be used for fragments that only have counts for
one valid fragment end.


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

combineFragEnds function

<code>combineFragEnds</code> combines the counts of both fragment ends. A
multiplication factor can be used for fragments that only have counts for
one valid fragment end.

combineFragEnds: Combine the counts of both fragment ends.

Description

Usage

Arguments

Value

See Also

Examples