createOffset: Create Offsets for Peak Calling

In plbaldoni/ZIMHMM: Improved Detection of Epigenomic Marks With Mixed Effects HMMs

Description

This function create offsets for peak calling. The current implementation can output three different set of offsets: total sum of read counts (method="sum"), smoothed MA trend (method="loess", similar to csaw), or median ratio (method="ratio", similar to DESeq2).

Usage

createOffset(ChIP, method = "sum", span = 0.3)

Arguments

ChIP	M*N matrix of ChIP read counts, where M is the number of windows in the analyzed genome and N is the number of experiments and replicates
method	either total sum of read counts (method="sum"), smoothed MA trend (method="loess"), or median ratio (method="ratio").
span	proportion of data to be used in the smoothing (see loessFit from limma, default 0.3)

Value

M*N matrix of offsets

Author(s)

Pedro L. Baldoni, [e-mail]

References

https://github.com/plbaldoni/ZIMHMM

Examples

data(Huvec)
ChIP = SummarizedExperiment::assay(Huvec,'ChIP')
offset = createOffset(ChIP,method="loess")

plbaldoni/ZIMHMM documentation built on Dec. 5, 2019, 11:43 p.m.