chr7Profiles {similaRpeak} | R Documentation

## 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)

### 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.

[Package similaRpeak version 1.20.0 Index]