Last data update: 2014.03.03

 R: Sites with the greatest evidence of transcription factor...
A549_CTCF_MYN_NarrowPeaks_partialR Documentation

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

Description

Sites representing the greatest evidence of enrichment for the CTCF transcription factor (DCC accession: ENCFF000MYN) for regions chr1:246000000-249250621 and chr10:10000000-12500000 from the Encyclopedia of DNA Elements (ENCODE) data (Dunham I et al. 2012).

Usage

data(A549_CTCF_MYN_NarrowPeaks_partial)

Format

A GRanges containing one entry per site.

Source

The Encyclopedia of DNA Elements (ENCODE) (DCC accession: ENCFF000MYN)

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_CTCF_MYN_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_CTCF_MYJ_NarrowPeaks_partial)
data(A549_CTCF_MYJ_Peaks_partial)
data(A549_CTCF_MYN_NarrowPeaks_partial)
data(A549_CTCF_MYN_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_CTCF_MYJ_Peaks_partial) <- rep("CTCF_MYJ",
                            length(A549_CTCF_MYJ_Peaks_partial))
names(A549_CTCF_MYJ_NarrowPeaks_partial) <- rep("CTCF_MYJ",
                            length(A549_CTCF_MYJ_NarrowPeaks_partial))
names(A549_CTCF_MYN_Peaks_partial) <-rep("CTCF_MYN",
                            length(A549_CTCF_MYN_Peaks_partial))
names(A549_CTCF_MYN_NarrowPeaks_partial) <- rep("CTCF_MYN",
                            length(A549_CTCF_MYN_NarrowPeaks_partial))

## Calculating consensus regions for chromosome 10
## 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).
## A peak from both experiments must be present in a region to
## be retained as a consensus region.
chrList <- Seqinfo("chr10", 135534747, NA)
findConsensusPeakRegions(
    narrowPeaks = c(A549_CTCF_MYJ_NarrowPeaks_partial,
                            A549_CTCF_MYN_NarrowPeaks_partial),
    peaks = c(A549_CTCF_MYJ_Peaks_partial,
                            A549_CTCF_MYN_Peaks_partial),
    chrInfo = chrList,
    extendingSize = 20,
    expandToFitPeakRegion = FALSE,
    shrinkToFitPeakRegion = FALSE,
    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_CTCF_MYN_NarrowPeaks_partial.Rd_%03d_medium.png", width=480, height=480)
> ### Name: A549_CTCF_MYN_NarrowPeaks_partial
> ### Title: Sites with the greatest evidence of transcription factor binding
> ###   for the CTCF transcription factor (for demonstration purpose)
> ### Aliases: A549_CTCF_MYN_NarrowPeaks_partial
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> ## Loading datasets
> data(A549_CTCF_MYJ_NarrowPeaks_partial)
> data(A549_CTCF_MYJ_Peaks_partial)
> data(A549_CTCF_MYN_NarrowPeaks_partial)
> data(A549_CTCF_MYN_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_CTCF_MYJ_Peaks_partial) <- rep("CTCF_MYJ",
+                             length(A549_CTCF_MYJ_Peaks_partial))
> names(A549_CTCF_MYJ_NarrowPeaks_partial) <- rep("CTCF_MYJ",
+                             length(A549_CTCF_MYJ_NarrowPeaks_partial))
> names(A549_CTCF_MYN_Peaks_partial) <-rep("CTCF_MYN",
+                             length(A549_CTCF_MYN_Peaks_partial))
> names(A549_CTCF_MYN_NarrowPeaks_partial) <- rep("CTCF_MYN",
+                             length(A549_CTCF_MYN_NarrowPeaks_partial))
> 
> ## Calculating consensus regions for chromosome 10
> ## 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).
> ## A peak from both experiments must be present in a region to
> ## be retained as a consensus region.
> chrList <- Seqinfo("chr10", 135534747, NA)
> findConsensusPeakRegions(
+     narrowPeaks = c(A549_CTCF_MYJ_NarrowPeaks_partial,
+                             A549_CTCF_MYN_NarrowPeaks_partial),
+     peaks = c(A549_CTCF_MYJ_Peaks_partial,
+                             A549_CTCF_MYN_Peaks_partial),
+     chrInfo = chrList,
+     extendingSize = 20,
+     expandToFitPeakRegion = FALSE,
+     shrinkToFitPeakRegion = FALSE,
+     minNbrExp = 2,
+     nbrThreads = 1)
$call
findConsensusPeakRegions(narrowPeaks = c(A549_CTCF_MYJ_NarrowPeaks_partial, 
    A549_CTCF_MYN_NarrowPeaks_partial), peaks = c(A549_CTCF_MYJ_Peaks_partial, 
    A549_CTCF_MYN_Peaks_partial), chrInfo = chrList, extendingSize = 20, 
    expandToFitPeakRegion = FALSE, shrinkToFitPeakRegion = FALSE, 
    minNbrExp = 2, nbrThreads = 1)

$consensusRanges
GRanges object with 14 ranges and 0 metadata columns:
       seqnames               ranges strand
          <Rle>            <IRanges>  <Rle>
   [1]    chr10 [11078547, 11078587]      *
   [2]    chr10 [11312707, 11312747]      *
   [3]    chr10 [11466689, 11466729]      *
   [4]    chr10 [11514308, 11514348]      *
   [5]    chr10 [11557783, 11557823]      *
   ...      ...                  ...    ...
  [10]    chr10 [11861956, 11861996]      *
  [11]    chr10 [12028764, 12028804]      *
  [12]    chr10 [12256844, 12256884]      *
  [13]    chr10 [12295050, 12295090]      *
  [14]    chr10 [12306319, 12306359]      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

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


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