ratio {ChIPSeqSpike} | R Documentation

## Result of method getRatio on the complete dataset

### Description

Result of method getRatio on the complete dataset.

### Usage

      data(ratio)

### Format

matrix

### Details

## Complete Dataset

The data used in this documentation represent a gold-standard example of the importance of using spike-in controls with ChIP-Seq experiments. It uses Drosophila Melanogaster chromatin as exogenous spike-in control to correct experimental biases. Without spike-in control and using only RPM normalization, proper differences of H3K79me2 histone modification in human Jurkat cells upon EPZ5676 inhibitor treatment are not observed [1].

This dataset is made of bigwig and bam files of H3K79me2 ChIP-Seq data and corresponding input DNA controls. Bam files contain data aligned to the Human reference genome Hg19 or to the Drosophila reference genome dm3. The latest is used to compute external spike-in scaling factors. All above mentioned data are available at 0, 50 and 100 percent EPZ5676 inhibitor treatment (see vignette for data references).

### References

[1] Orlando et al, "Quantitative ChIP-Seq normalization reveals global modulation of the epigenome", Cell Rep, 2014.

[Package ChIPSeqSpike version 1.6.0 Index]