Last data update: 2014.03.03

 R: Genomic regions with the greatest evidence of transcription...
A549_FOXA1_01_NarrowPeaks_partialR Documentation

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

Description

Genomic regions 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_NarrowPeaks_partial)

Format

A GRanges containing one entry per genomic regions. 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_Peaks_partial the associate sites 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 300 bp (2 * extendingSize)
## which is not extended to include all genomic regions.
## 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 = 150,
     expandToFitPeakRegion = 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_FOXA1_01_NarrowPeaks_partial.Rd_%03d_medium.png", width=480, height=480)
> ### Name: A549_FOXA1_01_NarrowPeaks_partial
> ### Title: Genomic regions with the greatest evidence of transcription
> ###   factor binding for the FOXA1 transcription factor (for demonstration
> ###   purpose)
> ### Aliases: A549_FOXA1_01_NarrowPeaks_partial
> ### Keywords: datasets
> 
> ### ** 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 300 bp (2 * extendingSize)
> ## which is not extended to include all genomic regions.
> ## 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 = 150,
+      expandToFitPeakRegion = FALSE,
+      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 = 150, 
    expandToFitPeakRegion = FALSE, minNbrExp = 2, nbrThreads = 1)

$consensusRanges
GRanges object with 11 ranges and 0 metadata columns:
       seqnames                 ranges strand
          <Rle>              <IRanges>  <Rle>
   [1]     chr1 [249120024, 249120324]      *
   [2]     chr1 [249120434, 249120734]      *
   [3]     chr1 [249123174, 249123474]      *
   [4]     chr1 [249132140, 249132440]      *
   [5]     chr1 [249153305, 249153605]      *
   [6]     chr1 [249167314, 249167614]      *
   [7]     chr1 [249167909, 249168209]      *
   [8]     chr1 [249200068, 249200368]      *
   [9]    chr10 [   179474,    179774]      *
  [10]    chr10 [   313079,    313379]      *
  [11]    chr10 [   343155,    343455]      *
  -------
  seqinfo: 2 sequences 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