Annotated Peaks

Description

TSS annotated putative STAT1-binding regions that are identified in un-stimulated cells using ChIP-seq technology (Robertson et al., 2007)

Usage

data(annotatedPeak)

Format

GRanges with slot start holding the start position of the peak, slot end holding the end position of the peak, slot names holding the id of the peak, slot strand holding the strands and slot space holding the chromosome location where the peak is located. In addition, the following variables are included.

feature

id of the feature such as ensembl gene ID

insideFeature

upstream: peak resides upstream of the feature; downstream: peak resides downstream of the feature; inside: peak resides inside the feature; overlapStart: peak overlaps with the start of the feature; overlapEnd: peak overlaps with the end of the feature; includeFeature: peak include the feature entirely

distancetoFeature

distance to the nearest feature such as transcription start site

start_position

start position of the feature such as gene

end_position

end position of the feature such as the gene

Details

obtained by data(TSS.human.GRCh37)

data(myPeakList)

annotatePeakInBatch(myPeakList, AnnotationData = TSS.human.GRCh37, output="b", multiple=F)

Examples

data(annotatedPeak)
str(annotatedPeak) 
if (interactive()) {
y = annotatedPeak$distancetoFeature[!is.na(annotatedPeak$distancetoFeature)]
hist(as.numeric(as.character(y)), 
     xlab="Distance To Nearest TSS", main="", breaks=1000, 
ylim=c(0, 50), xlim=c(min(as.numeric(as.character(y)))-100, 
max(as.numeric(as.character(y)))+100))
}

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.
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Type 'license()' or 'licence()' for distribution details.

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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(ChIPpeakAnno)
Loading required package: grid
Loading required package: IRanges
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: 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: Biostrings
Loading required package: XVector
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: VennDiagram
Loading required package: futile.logger

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ChIPpeakAnno/annotatedPeak.Rd_%03d_medium.png", width=480, height=480)
> ### Name: annotatedPeak
> ### Title: Annotated Peaks
> ### Aliases: annotatedPeak
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(annotatedPeak)
> str(annotatedPeak) 
Formal class 'GRanges' [package "GenomicRanges"] with 6 slots
  ..@ seqnames       :Formal class 'Rle' [package "S4Vectors"] with 4 slots
  .. .. ..@ values         : Factor w/ 24 levels "1","10","11",..: 1 2 3 4 5 6 7 8 9 10 ...
  .. .. ..@ lengths        : int [1:24] 1727 136 504 771 493 120 98 914 200 1000 ...
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ ranges         :Formal class 'IRanges' [package "IRanges"] with 6 slots
  .. .. ..@ start          : int [1:13409] 100272801 108906026 110107267 110680469 110682125 110756823 112963701 113017841 113148443 113280036 ...
  .. .. ..@ width          : int [1:13409] 100 100 100 100 100 100 100 100 100 100 ...
  .. .. ..@ NAMES          : chr [1:13409] "X1_11_100272487.ENSG00000202254" "X1_11_108905539.ENSG00000186086" "X1_11_110106925.ENSG00000065135" "X1_11_110679983.ENSG00000197106" ...
  .. .. ..@ elementType    : chr "integer"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ strand         :Formal class 'Rle' [package "S4Vectors"] with 4 slots
  .. .. ..@ values         : Factor w/ 3 levels "+","-","*": 1 2 1 2 1 2 1 2 1 2 ...
  .. .. ..@ lengths        : int [1:1069] 657 595 3 3 2 1 1 1 2 1 ...
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
  .. .. ..@ rownames       : NULL
  .. .. ..@ nrows          : int 13409
  .. .. ..@ listData       :List of 8
  .. .. .. ..$ peak                    : chr [1:13409] "1_11_100272487" "1_11_108905539" "1_11_110106925" "1_11_110679983" ...
  .. .. .. ..$ feature                 : chr [1:13409] "ENSG00000202254" "ENSG00000186086" "ENSG00000065135" "ENSG00000197106" ...
  .. .. .. ..$ start_position          : num [1:13409] 1.00e+08 1.09e+08 1.10e+08 1.11e+08 1.11e+08 ...
  .. .. .. ..$ end_position            : num [1:13409] 1.00e+08 1.09e+08 1.10e+08 1.11e+08 1.11e+08 ...
  .. .. .. ..$ insideFeature           : chr [1:13409] "downstream" "upstream" "inside" "upstream" ...
  .. .. .. ..$ distancetoFeature       : num [1:13409] 15582 -12410 16033 -12640 -10984 ...
  .. .. .. ..$ shortestDistance        : num [1:13409] 15491 12310 16033 12540 10884 ...
  .. .. .. ..$ fromOverlappingOrNearest: chr [1:13409] "NearestStart" "NearestStart" "NearestStart" "NearestStart" ...
  .. .. ..@ elementType    : chr "ANY"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ seqinfo        :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots
  .. .. ..@ seqnames   : chr [1:24] "1" "10" "11" "12" ...
  .. .. ..@ seqlengths : int [1:24] NA NA NA NA NA NA NA NA NA NA ...
  .. .. ..@ is_circular: logi [1:24] NA NA NA NA NA NA ...
  .. .. ..@ genome     : chr [1:24] NA NA NA NA ...
  ..@ metadata       : list()
> #if (interactive()) {
> y = annotatedPeak$distancetoFeature[!is.na(annotatedPeak$distancetoFeature)]
> hist(as.numeric(as.character(y)), 
+      xlab="Distance To Nearest TSS", main="", breaks=1000, 
+ ylim=c(0, 50), xlim=c(min(as.numeric(as.character(y)))-100, 
+ max(as.numeric(as.character(y)))+100))
> #}
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>