Last data update: 2014.03.03

 R: Ranges with the greatest evidence of transcription factor...
A549_NR3C1_CFQ_NarrowPeaks_partialR Documentation

Ranges with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFQ). For demonstration purpose.

Description

Ranges representing the greatest evidence of enrichment for the NR3C1 transcription factor (DCC accession: ENCFF002CFQ) for regions chr2:40000000-50000000 and chr3:10000000-13000000 from the Encyclopedia of DNA Elements (ENCODE) data (Dunham I et al. 2012).

Usage

data(A549_NR3C1_CFQ_NarrowPeaks_partial)

Format

A GRanges containing one entry per site. The ranges are surronding the peaks present in the dataset A549_NR3C1_CFQ_Peaks_partial.

Details

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

Source

The Encyclopedia of DNA Elements (ENCODE) (DCC accession: ENCFF002CFQ)

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_CFQ_Peaks_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_CFS_NarrowPeaks_partial)
data(A549_NR3C1_CFS_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_CFS_NarrowPeaks_partial) <-rep("NR3C1_CFS",
                            length(A549_NR3C1_CFS_NarrowPeaks_partial))
names(A549_NR3C1_CFS_Peaks_partial) <- rep("NR3C1_CFS",
                            length(A549_NR3C1_CFS_Peaks_partial))

## Calculating consensus regions for chromosome 3
## with a default region size of 300 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("chr3"), c(198022430), NA)
findConsensusPeakRegions(
    narrowPeaks = c(A549_NR3C1_CFQ_NarrowPeaks_partial,
                            A549_NR3C1_CFS_NarrowPeaks_partial),
    peaks = c(A549_NR3C1_CFQ_Peaks_partial,
                            A549_NR3C1_CFS_Peaks_partial),
    chrInfo = chrList,
    extendingSize = 150,
    expandToFitPeakRegion = FALSE,
    shrinkToFitPeakRegion = TRUE,
    minNbrExp = 2,
    nbrThreads = 1)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(consensusSeekeR)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: BiocParallel
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/consensusSeekeR/A549_NR3C1_CFQ_NarrowPeaks_partial.Rd_%03d_medium.png", width=480, height=480)
> ### Name: A549_NR3C1_CFQ_NarrowPeaks_partial
> ### Title: Ranges with the greatest evidence of transcription factor
> ###   binding for the NR3C1 transcription factor from ENCODE (DDC
> ###   accession: ENCFF002CFQ). For demonstration purpose.
> ### Aliases: A549_NR3C1_CFQ_NarrowPeaks_partial
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> ## Loading datasets
> data(A549_NR3C1_CFQ_NarrowPeaks_partial)
> data(A549_NR3C1_CFQ_Peaks_partial)
> data(A549_NR3C1_CFS_NarrowPeaks_partial)
> data(A549_NR3C1_CFS_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_CFS_NarrowPeaks_partial) <-rep("NR3C1_CFS",
+                             length(A549_NR3C1_CFS_NarrowPeaks_partial))
> names(A549_NR3C1_CFS_Peaks_partial) <- rep("NR3C1_CFS",
+                             length(A549_NR3C1_CFS_Peaks_partial))
> 
> ## Calculating consensus regions for chromosome 3
> ## with a default region size of 300 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("chr3"), c(198022430), NA)
> findConsensusPeakRegions(
+     narrowPeaks = c(A549_NR3C1_CFQ_NarrowPeaks_partial,
+                             A549_NR3C1_CFS_NarrowPeaks_partial),
+     peaks = c(A549_NR3C1_CFQ_Peaks_partial,
+                             A549_NR3C1_CFS_Peaks_partial),
+     chrInfo = chrList,
+     extendingSize = 150,
+     expandToFitPeakRegion = FALSE,
+     shrinkToFitPeakRegion = TRUE,
+     minNbrExp = 2,
+     nbrThreads = 1)
$call
findConsensusPeakRegions(narrowPeaks = c(A549_NR3C1_CFQ_NarrowPeaks_partial, 
    A549_NR3C1_CFS_NarrowPeaks_partial), peaks = c(A549_NR3C1_CFQ_Peaks_partial, 
    A549_NR3C1_CFS_Peaks_partial), chrInfo = chrList, extendingSize = 150, 
    expandToFitPeakRegion = FALSE, shrinkToFitPeakRegion = TRUE, 
    minNbrExp = 2, nbrThreads = 1)

$consensusRanges
GRanges object with 0 ranges and 0 metadata columns:
   seqnames    ranges strand
      <Rle> <IRanges>  <Rle>
  -------
  seqinfo: no sequences

attr(,"class")
[1] "consensusRanges"
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO