Sites with the greatest evidence of transcription factor binding for the FOXA1 transcription factor (for demonstration purpose)

Sites representing the greatest evidence of enrichment for the FOXA1 transcription factor (DCC accession: ENCFF000NAH) for regions chr1:249120200-249250621 and chr10:1-370100 from the Encyclopedia of DNA Elements (ENCODE) data (Dunham I et al. 2012).

data(A549_FOXA1_01_Peaks_partial)

Format

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

Source

The Encyclopedia of DNA Elements (ENCODE) (DCC accession: ENCFF000NAH)

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_FOXA1_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_FOSL2_01_Peaks_partial)
data(A549_FOXA1_01_NarrowPeaks_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 both chromosomes 1 and 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("chr1", "chr10"), c(249250621, 135534747), 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 = 50,
    expandToFitPeakRegion = TRUE,
    shrinkToFitPeakRegion = TRUE,
    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 = 50, 
#>     expandToFitPeakRegion = TRUE, shrinkToFitPeakRegion = TRUE, 
#>     minNbrExp = 2, nbrThreads = 1)
#> 
#> $consensusRanges
#> GRanges object with 6 ranges and 0 metadata columns:
#>       seqnames              ranges strand
#>          <Rle>           <IRanges>  <Rle>
#>   [1]     chr1 249123089-249123453      *
#>   [2]     chr1 249167266-249167579      *
#>   [3]     chr1 249167825-249168802      *
#>   [4]     chr1 249200099-249200329      *
#>   [5]    chr10       179402-179820      *
#>   [6]    chr10       343173-343457      *
#>   -------
#>   seqinfo: 2 sequences from an unspecified genome; no seqlengths
#> 
#> attr(,"class")
#> [1] "consensusRanges"