similaRpeak (version 1.4.2)

chr7Profiles: ChIP-Seq profiles of region chr7:61968807-61969730 related to enhancers H3K27ac and H3K4me1 (for demonstration purpose)

Description

ChIP-Seq profiles of region chr7:61968807-61969730 of two histone post-transcriptional modifications linked to highly active enhancers H3K27ac (DCC accession: ENCFF000ASG) and H3K4me1 (DCC accession: ENCFF000ARY) from the Encyclopedia of DNA Elements (ENCODE) data (Dunham I et al. 2012).

Usage

data(chr7Profiles)

source

The Encyclopedia of DNA Elements (ENCODE) data

References

Dunham I, Kundaje A, Aldred SF, et al. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74.

See Also

• MetricFactory{for using a interface to calculate all available metrics separately.}
• similarity{for calculating all available metrics between two ChIP-Seq profiles.}

Examples

data(chr7Profiles)

## Calculating all metrics for the "chr7.61968807.61969730" region 
metrics <- similarity(chr7Profiles$chr7.61968807.61969730$H3K4me1, 
                        chr7Profiles$chr7.61968807.61969730$H3K27ac, 
                        ratioAreaThreshold=10, 
                        ratioMaxMaxThreshold=4, 
                        ratioIntersectThreshold=5, 
                        ratioNormalizedIntersectThreshold=2,
                        diffPosMaxThresholdMinValue=10, 
                        diffPosMaxThresholdMaxDiff=100, 
                        diffPosMaxTolerance=0.10)
metrics


## You can refer to the vignette to see more examples using ChIP-Seq profiles
## extracted from the Encyclopedia of DNA Elements (ENCODE) data.