Sites with the greatest evidence of transcription factor binding for the CTCF transcription factor (for demonstration purpose)

Sites representing the greatest evidence of enrichment for the CTCF transcription factor (DCC accession: ENCFF000MYJ) 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_MYJ_Peaks_partial)

Format

A GRanges containing one entry per site.

Source

The Encyclopedia of DNA Elements (ENCODE) (DCC accession: ENCFF000MYJ)

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

• A549_CTCF_MYJ_NarrowPeaks_partial the associate genomic regions dataset.

• findConsensusPeakRegions for extracting regions sharing the same features in more than one experiment.

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(c("chr10"), c(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"