Sites representing the greatest evidence of enrichment for the CTCF transcription factor (DCC accession: ENCFF000MYN) for regions chr1:246000000-249250621 and chr10:10000000-12500000 from the Encyclopedia of DNA Elements (ENCODE) data (Dunham I et al. 2012).

data(A549_CTCF_MYN_NarrowPeaks_partial)

Format

A GRanges containing one entry per site.

Source

The Encyclopedia of DNA Elements (ENCODE) (DCC accession: ENCFF000MYN)

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

Examples


## Loading datasets
data(A549_CTCF_MYJ_NarrowPeaks_partial)
data(A549_CTCF_MYJ_Peaks_partial)
data(A549_CTCF_MYN_NarrowPeaks_partial)
data(A549_CTCF_MYN_Peaks_partial)

## Assigning experiment name to each row of the dataset.
## NarrowPeak and Peak datasets from the same experiment must
## have identical names.
names(A549_CTCF_MYJ_Peaks_partial) <- rep("CTCF_MYJ",
                            length(A549_CTCF_MYJ_Peaks_partial))
names(A549_CTCF_MYJ_NarrowPeaks_partial) <- rep("CTCF_MYJ",
                            length(A549_CTCF_MYJ_NarrowPeaks_partial))
names(A549_CTCF_MYN_Peaks_partial) <-rep("CTCF_MYN",
                            length(A549_CTCF_MYN_Peaks_partial))
names(A549_CTCF_MYN_NarrowPeaks_partial) <- rep("CTCF_MYN",
                            length(A549_CTCF_MYN_NarrowPeaks_partial))

## Calculating consensus regions for chromosome 10
## with a default region size of 40 bp (2 * extendingSize)
## which is extended to include all genomic regions for the closest
## peak to the median position of all peaks included in the region (for each
## experiment).
## A peak from both experiments must be present in a region to
## be retained as a consensus region.
chrList <- Seqinfo("chr10", 135534747, NA)
findConsensusPeakRegions(
    narrowPeaks = c(A549_CTCF_MYJ_NarrowPeaks_partial,
                            A549_CTCF_MYN_NarrowPeaks_partial),
    peaks = c(A549_CTCF_MYJ_Peaks_partial,
                            A549_CTCF_MYN_Peaks_partial),
    chrInfo = chrList,
    extendingSize = 20,
    expandToFitPeakRegion = FALSE,
    shrinkToFitPeakRegion = FALSE,
    minNbrExp = 2,
    nbrThreads = 1)
#> $call
#> findConsensusPeakRegions(narrowPeaks = c(A549_CTCF_MYJ_NarrowPeaks_partial, 
#>     A549_CTCF_MYN_NarrowPeaks_partial), peaks = c(A549_CTCF_MYJ_Peaks_partial, 
#>     A549_CTCF_MYN_Peaks_partial), chrInfo = chrList, extendingSize = 20, 
#>     expandToFitPeakRegion = FALSE, shrinkToFitPeakRegion = FALSE, 
#>     minNbrExp = 2, nbrThreads = 1)
#> 
#> $consensusRanges
#> GRanges object with 14 ranges and 0 metadata columns:
#>        seqnames            ranges strand
#>           <Rle>         <IRanges>  <Rle>
#>    [1]    chr10 11078547-11078587      *
#>    [2]    chr10 11312707-11312747      *
#>    [3]    chr10 11466689-11466729      *
#>    [4]    chr10 11514308-11514348      *
#>    [5]    chr10 11557783-11557823      *
#>    ...      ...               ...    ...
#>   [10]    chr10 11861956-11861996      *
#>   [11]    chr10 12028764-12028804      *
#>   [12]    chr10 12256844-12256884      *
#>   [13]    chr10 12295050-12295090      *
#>   [14]    chr10 12306319-12306359      *
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
#> 
#> attr(,"class")
#> [1] "consensusRanges"