Ste12-binding sites from biological replicate 1 in yeast (see reference)

Description

Ste12-binding sites from biological replicate 1 in yeast (see reference)

Usage

data(Peaks.Ste12.Replicate1)

Format

RangedData with slot rownames containing the ID of peak as character, slot start containing the start position of the peak, slot end containing the end position of the peak and space containing the chromosome where the peak is located.

References

Philippe Lefranois, Ghia M Euskirchen, Raymond K Auerbach, Joel Rozowsky, Theodore Gibson, Christopher M Yellman, Mark Gerstein and Michael Snyder (2009) Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing BMC Genomics 10:37

Examples

data(Peaks.Ste12.Replicate1)
str(Peaks.Ste12.Replicate1)

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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Type 'demo()' for some demos, 'help()' for on-line help, or
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> 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/Peaks.Ste12.Replicate1.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Peaks.Ste12.Replicate1
> ### Title: Ste12-binding sites from biological replicate 1 in yeast (see
> ###   reference)
> ### Aliases: Peaks.Ste12.Replicate1
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Peaks.Ste12.Replicate1)
> str(Peaks.Ste12.Replicate1)
Formal class 'RangedData' [package "IRanges"] with 5 slots
  ..@ ranges         :Formal class 'CompressedIRangesList' [package "IRanges"] with 5 slots
  .. .. ..@ elementType    : chr "IRanges"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  .. .. ..@ partitioning   :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots
  .. .. .. .. ..@ end            : int [1:16] 13 56 74 154 173 220 260 283 336 365 ...
  .. .. .. .. ..@ NAMES          : chr [1:16] "chr1" "chr10" "chr11" "chr12" ...
  .. .. .. .. ..@ elementType    : chr "integer"
  .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. ..@ metadata       : list()
  .. .. ..@ unlistData     :Formal class 'IRanges' [package "IRanges"] with 6 slots
  .. .. .. .. ..@ start          : int [1:668] 67961 67961 141316 141316 168663 168663 70875 139084 28599 92532 ...
  .. .. .. .. ..@ width          : int [1:668] 2294 2294 612 612 509 509 529 627 332 200 ...
  .. .. .. .. ..@ NAMES          : chr [1:668] "22" "23" "240" "241" ...
  .. .. .. .. ..@ elementType    : chr "integer"
  .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. ..@ metadata       : list()
  ..@ values         :Formal class 'CompressedSplitDataFrameList' [package "IRanges"] with 5 slots
  .. .. ..@ elementType    : chr "DataFrame"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  .. .. ..@ partitioning   :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots
  .. .. .. .. ..@ end            : int [1:16] 13 56 74 154 173 220 260 283 336 365 ...
  .. .. .. .. ..@ NAMES          : chr [1:16] "chr1" "chr10" "chr11" "chr12" ...
  .. .. .. .. ..@ elementType    : chr "integer"
  .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. ..@ metadata       : list()
  .. .. ..@ unlistData     :Formal class 'DataFrame' [package "IRanges"] with 6 slots
  .. .. .. .. ..@ rownames       : chr [1:668] "22" "23" "240" "241" ...
  .. .. .. .. ..@ nrows          : int 668
  .. .. .. .. ..@ listData       :List of 1
  .. .. .. .. .. ..$ strand: int [1:668] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. .. ..@ elementType    : chr "ANY"
  .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. ..@ metadata       : list()
  ..@ elementType    : chr "ANY"
  ..@ elementMetadata: NULL
  ..@ metadata       : list()
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>