R: Genomic regions with the greatest evidence of transcription...
A549_FOSL2_01_NarrowPeaks_partial
R Documentation
Genomic regions with the greatest evidence of transcription factor binding
for the FOSL2 transcription factor (for demonstration purpose)
Description
Genomic regions representing the greatest evidence of enrichment for
the FOSL2 transcription factor (DCC accession: ENCFF000MZT)
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_FOSL2_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:
ENCFF000MZT)
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_FOSL2_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 chromosome 10 only
## with a default region size of 200 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("chr10", 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 = 100,
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_FOSL2_01_NarrowPeaks_partial.Rd_%03d_medium.png", width=480, height=480)
> ### Name: A549_FOSL2_01_NarrowPeaks_partial
> ### Title: Genomic regions with the greatest evidence of transcription
> ### factor binding for the FOSL2 transcription factor (for demonstration
> ### purpose)
> ### Aliases: A549_FOSL2_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 chromosome 10 only
> ## with a default region size of 200 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("chr10", 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 = 100,
+ expandToFitPeakRegion = FALSE,
+ shrinkToFitPeakRegion = TRUE,
+ 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 = 100,
expandToFitPeakRegion = FALSE, shrinkToFitPeakRegion = TRUE,
minNbrExp = 2, nbrThreads = 1)
$consensusRanges
GRanges object with 3 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr10 [179524, 179724] *
[2] chr10 [313129, 313329] *
[3] chr10 [343205, 343405] *
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
attr(,"class")
[1] "consensusRanges"
>
>
>
>
>
>
> dev.off()
null device
1
>