chr7Profiles: ChIP-Seq profiles of region chr7:61968807-61969730 related to...

In similaRpeak: Metrics to estimate a level of similarity between two ChIP-Seq profiles

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)

Format

A list with 1 entry. The entry is a list of 2 ChIP-Seq profiles, one per active enhancer (H3K27ac and H3K4me1).The 2 ChIP-Seq profiles are of identical length and specific to a genomic region. Each ChiP-Seq profile is a numerical vector containing the profiles values at each position, as reported in reads per million (RPM).

• chr7Profiles a list containing all demo ChIP-Seq profiles

• chr7Profiles$chr7.61968807.61969730 a list containing 2 ChIP-Seq profiles for the genomic region chr7:6196880-61969730

• demoProfiles$chr7.61968807.61969730$H3K27ac a numeric vector containing the profiles values related to the enhancer H3K27ac, as reported in reads per million (RPM). The first entry of the vector is for position chr7:61968807 while the last entry is for position chr7:61969730

• demoProfiles$chr7.61968807.61969730$H3K4me1 a numeric vector containing the profiles values related to the enhancer H3K4me1, as reported in reads per million (RPM). The first entry of the vector is for position chr7:61968807 while the last entry is for position chr7:61969730

Source

The Encyclopedia of DNA Elements (ENCODE) (DCC accession: ENCFF000MZT)

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

• demoProfiles ChIP-seq profiles related to enhancers H3K27ac and H3K4me1 (for demonstration purpose)

• 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.

similaRpeak documentation built on Nov. 8, 2020, 6:56 p.m.