Alignments of ChIP-seq data to yeast chromosome XIV

Description

MAQ alignments to yeast chromosome XIV of ChIP-seq data of ORC-binding sites in yeast from Eaton et al. 2010

Usage

data(orcAlignsRep1)
data(orcAlignsRep2)

Details

This is the subset of alignments from two ChIP-seq replicates of origin recognition complex (ORC) binding to chromosome XIV of Saccharomyces cerevisiae. The alignments were created using MAQ (Li et al. 2008) alignment software with a maximum mismatch of 3 bases and a minimum Phred quality score of 35.

Source

MAQ alignments extracted from ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM424nnn/GSM424494/GSM424494_wt_G2_orc_chip_rep1.mapview.txt.gz and ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM424nnn/GSM424494/GSM424494_wt_G2_orc_chip_rep2.mapview.txt.gz

References

Conserved nucleosome positioning defines replication origins. Eaton ML, Galani K, Kang S, Bell SP, MacAlpine DM. Genes Dev. 2010 Apr 15;24(8):748-53.

Examples

data(orcAlignsRep1)
data(orcAlignsRep2)

orcAlignsRep1
orcAlignsRep2

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(EatonEtAlChIPseq)
Loading required package: GenomicRanges
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: IRanges
Loading required package: GenomeInfoDb
Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: Biostrings
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: rtracklayer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/EatonEtAlChIPseq/orcAligns.Rd_%03d_medium.png", width=480, height=480)
> ### Name: orcAligns
> ### Title: Alignments of ChIP-seq data to yeast chromosome XIV
> ### Aliases: orcAlignsRep1 orcAlignsRep2
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(orcAlignsRep1)
> data(orcAlignsRep2)
> 
> orcAlignsRep1
class: AlignedRead
length: 478774 reads; width: 39 cycles
chromosome: chrXIV chrXIV ... chrXIV chrXIV 
position: 2 4 ... 784295 784295 
strand: + - ... + + 
alignQuality: IntegerQuality 
alignData varLabels: nMismatchBestHit mismatchQuality nExactMatch24 nOneMismatch24 
> orcAlignsRep2
class: AlignedRead
length: 357022 reads; width: 39 cycles
chromosome: chrXIV chrXIV ... chrXIV chrXIV 
position: 3 6 ... 784295 784295 
strand: + - ... - - 
alignQuality: IntegerQuality 
alignData varLabels: nMismatchBestHit mismatchQuality nExactMatch24 nOneMismatch24 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>