Sites with the greatest evidence of transcription factor binding for the FOSL2 transcription factor (for demonstration purpose)

Sites representing the greatest evidence of enrichment for the FOSL2 transcription factor (DCC accession: ENCFF000MZT) for regions chr1:249120200-249250621 and chr10:1-370100 from the Encyclopedia of DNA Elements (ENCODE) data (Dunham I et al. 2012).

data(A549_FOSL2_01_Peaks_partial)

Format

A GRanges containing one entry per site. Each row of GRanges has the same row name which represent the name of the experiment.

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

• A549_FOSL2_01_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_FOSL2_01_NarrowPeaks_partial)
data(A549_FOXA1_01_NarrowPeaks_partial)
data(A549_FOSL2_01_Peaks_partial)
data(A549_FOXA1_01_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_FOXA1_01_Peaks_partial) <- rep("FOXA1_01",
                            length(A549_FOXA1_01_Peaks_partial))
names(A549_FOXA1_01_NarrowPeaks_partial) <- rep("FOXA1_01",
                            length(A549_FOXA1_01_NarrowPeaks_partial))
names(A549_FOSL2_01_Peaks_partial) <-rep("FOSL2_01",
                            length(A549_FOSL2_01_Peaks_partial))
names(A549_FOSL2_01_NarrowPeaks_partial) <- rep("FOSL2_01",
                            length(A549_FOSL2_01_NarrowPeaks_partial))

## Calculating consensus regions for chromosome 1 only
## with a default region size of 400 bp (2 * extendingSize)
## which is extended to include all genomic regions of the
## closest peak (for each experiment).
## A peak from both experiments must be present in a region to
## be retained as a consensus region.
chrList <- Seqinfo("chr1", 249250621, NA)
findConsensusPeakRegions(
    narrowPeaks = c(A549_FOXA1_01_NarrowPeaks_partial,
                            A549_FOSL2_01_NarrowPeaks_partial),
    peaks = c(A549_FOXA1_01_Peaks_partial,
                            A549_FOSL2_01_Peaks_partial),
    chrInfo = chrList,
    extendingSize = 200,
    expandToFitPeakRegion = TRUE,
    shrinkToFitPeakRegion = FALSE,
    minNbrExp = 2,
    nbrThreads = 1)
#> $call
#> findConsensusPeakRegions(narrowPeaks = c(A549_FOXA1_01_NarrowPeaks_partial, 
#>     A549_FOSL2_01_NarrowPeaks_partial), peaks = c(A549_FOXA1_01_Peaks_partial, 
#>     A549_FOSL2_01_Peaks_partial), chrInfo = chrList, extendingSize = 200, 
#>     expandToFitPeakRegion = TRUE, shrinkToFitPeakRegion = FALSE, 
#>     minNbrExp = 2, nbrThreads = 1)
#> 
#> $consensusRanges
#> GRanges object with 8 ranges and 0 metadata columns:
#>       seqnames              ranges strand
#>          <Rle>           <IRanges>  <Rle>
#>   [1]     chr1 249119914-249120374      *
#>   [2]     chr1 249120384-249121174      *
#>   [3]     chr1 249123089-249123524      *
#>   [4]     chr1 249132090-249132673      *
#>   [5]     chr1 249153243-249153673      *
#>   [6]     chr1 249167264-249167664      *
#>   [7]     chr1 249167825-249168802      *
#>   [8]     chr1 249200018-249200418      *
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
#> 
#> attr(,"class")
#> [1] "consensusRanges"