R: Sites with the greatest evidence of transcription factor...
A549_CTCF_MYJ_Peaks_partial
R 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: ENCFF000MYJ)
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_MYJ_Peaks_partial)
Format
A GRanges containing one entry per site.
Source
The Encyclopedia of DNA Elements (ENCODE) (DCC accession:
ENCFF000MYJ)
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_MYJ_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_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(c("chr10"), c(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)
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'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
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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_MYJ_Peaks_partial.Rd_%03d_medium.png", width=480, height=480)
> ### Name: A549_CTCF_MYJ_Peaks_partial
> ### Title: Sites with the greatest evidence of transcription factor binding
> ### for the CTCF transcription factor (for demonstration purpose)
> ### Aliases: A549_CTCF_MYJ_Peaks_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(c("chr10"), c(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"
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> dev.off()
null device
1
>