jg.getDba

is the filename of samplesheet to be loaded

jg.experimentSampleSheet

is the peak width in bp from summits (optional)

dbaSummits

are the parameters to be passed to DiffBinds dba.count function

Generates a DiffBind object from a valid SampleSheet with the required
data for normalisation. No examples are provided as BAM files are not
included in this package.

Counts

load

Diffbind

samplesheet

Inter-sample condition variability is a key challenge of normalising ChIP-seq data. This implementation uses either spike-in or a second factor as a control for normalisation. Input can either be from 'DiffBind' or a matrix formatted for 'DESeq2'. The output is either a 'DiffBind' object or the default 'DESeq2' output. Either can then be processed as normal. Supporting manuscript Guertin, Markowetz and Holding (2017) <doi:10.1101/182261>.

jg.getDba: jg.getDba

Description

Usage

Arguments