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_NarrowPeaks_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_Peaks_partial the associate genomic peaks dataset.

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

A549_CTCF_MYJ_NarrowPeaks_partial

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 100 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 = 50,
    expandToFitPeakRegion = TRUE,
    shrinkToFitPeakRegion = TRUE,
    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 = 50, 
#>     expandToFitPeakRegion = TRUE, shrinkToFitPeakRegion = TRUE, 
#>     minNbrExp = 2, nbrThreads = 1)
#> 
#> $consensusRanges
#> GRanges object with 18 ranges and 0 metadata columns:
#>        seqnames            ranges strand
#>           <Rle>         <IRanges>  <Rle>
#>    [1]    chr10 11078504-11078657      *
#>    [2]    chr10 11312608-11312835      *
#>    [3]    chr10 11466554-11466858      *
#>    [4]    chr10 11476458-11476629      *
#>    [5]    chr10 11514163-11514439      *
#>    ...      ...               ...    ...
#>   [14]    chr10 12172340-12172644      *
#>   [15]    chr10 12256640-12257000      *
#>   [16]    chr10 12294953-12295182      *
#>   [17]    chr10 12306222-12306516      *
#>   [18]    chr10 12307825-12308038      *
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
#> 
#> attr(,"class")
#> [1] "consensusRanges"