Sites with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFR). For demonstration purpose.

Sites representing the greatest evidence of enrichment for the NR3C1 transcription factor (DCC accession: ENCFF002CFR) for regions chr2:40000000-50000000 and chr3:10000000-13000000 from the Encyclopedia of DNA Elements (ENCODE) data (Dunham I et al. 2012).

data(A549_NR3C1_CFR_Peaks_partial)

Format

A GRanges containing one entry per site. The peaks are surronded by ranges present in the dataset A549_NR3C1_CFR_NarrowPeaks_partial.

Source

The Encyclopedia of DNA Elements (ENCODE) (DCC accession: ENCFF002CFR)

Details

The peaks and ranges have been obtained using an optimal IDR analysis done on all replicates.

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_NR3C1_CFR_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_NR3C1_CFQ_NarrowPeaks_partial)
data(A549_NR3C1_CFQ_Peaks_partial)
data(A549_NR3C1_CFR_NarrowPeaks_partial)
data(A549_NR3C1_CFR_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_NR3C1_CFQ_NarrowPeaks_partial) <- rep("NR3C1_CFQ",
                            length(A549_NR3C1_CFQ_NarrowPeaks_partial))
names(A549_NR3C1_CFQ_Peaks_partial) <- rep("NR3C1_CFQ",
                            length(A549_NR3C1_CFQ_Peaks_partial))
names(A549_NR3C1_CFR_NarrowPeaks_partial) <-rep("NR3C1_CFR",
                            length(A549_NR3C1_CFR_NarrowPeaks_partial))
names(A549_NR3C1_CFR_Peaks_partial) <- rep("NR3C1_CFR",
                            length(A549_NR3C1_CFR_Peaks_partial))

## Calculating consensus regions for chromosome 2
## 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).
## Peaks from both experiments must be present in a region to
## be retained as a consensus region.
chrList <- Seqinfo(c("chr2"), c(243199373), NA)
findConsensusPeakRegions(
    narrowPeaks = c(A549_NR3C1_CFQ_NarrowPeaks_partial,
                            A549_NR3C1_CFR_NarrowPeaks_partial),
    peaks = c(A549_NR3C1_CFQ_Peaks_partial,
                            A549_NR3C1_CFR_Peaks_partial),
    chrInfo = chrList,
    extendingSize = 20,
    expandToFitPeakRegion = TRUE,
    shrinkToFitPeakRegion = FALSE,
    minNbrExp = 2,
    nbrThreads = 1)
#> $call
#> findConsensusPeakRegions(narrowPeaks = c(A549_NR3C1_CFQ_NarrowPeaks_partial, 
#>     A549_NR3C1_CFR_NarrowPeaks_partial), peaks = c(A549_NR3C1_CFQ_Peaks_partial, 
#>     A549_NR3C1_CFR_Peaks_partial), chrInfo = chrList, extendingSize = 20, 
#>     expandToFitPeakRegion = TRUE, shrinkToFitPeakRegion = FALSE, 
#>     minNbrExp = 2, nbrThreads = 1)
#> 
#> $consensusRanges
#> GRanges object with 1 range and 0 metadata columns:
#>       seqnames            ranges strand
#>          <Rle>         <IRanges>  <Rle>
#>   [1]     chr2 40662093-49534300      *
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
#> 
#> attr(,"class")
#> [1] "consensusRanges"