A549_FOXA1_01_Peaks_partial: Sites with the greatest evidence of transcription factor...

In consensusSeekeR: Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges

Description

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).

Usage

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)

consensusSeekeR documentation built on Nov. 8, 2020, 4:54 p.m.