Toy RNA-seq data from RGASP project.

Description

The paired-end RNA-seq data is from the RGASP project sample K562_2x75 (replicate 1, lane 1) and was obtained at ftp://ftp.sanger.ac.uk/pub/gencode/rgasp/RGASP1/inputdata/human_fastq. Reads were aligned against hg19 with tophat 2.0.2 and bowtie 0.12.5, setting the insert size at -r 200, and imported into R using scanBam from package Rsamtools. For illustration purposes, we selected reads mapping to a few genes only (namely, the genes that were also selected for the toy genome annotation in data(hg19DB).

Usage

data(K562.r1l1)

Format

A list indicating read id, chromosome, start and end locations and the position of the pair, as returned by scanBam.

Source

ftp://ftp.sanger.ac.uk/pub/gencode/rgasp/RGASP1/inputdata/human_fastq

References

C Trapnell, L Pachter, SL Salzberg. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 2009, 25, 1105-1111. doi=10.1093/bioinformatics/btp120.

B Langmead, C Trapnell, M Pop, SL Salzberg. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 2009, 10:R25.

Examples

data(K562.r1l1)
names(K562.r1l1)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(casper)
Loading required package: Biobase
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

Welcome to Bioconductor

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

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
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/casper/K562.r1l1.Rd_%03d_medium.png", width=480, height=480)
> ### Name: K562.r1l1
> ### Title: Toy RNA-seq data from RGASP project.
> ### Aliases: K562.r1l1
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(K562.r1l1)
> names(K562.r1l1)
 [1] "qname"  "flag"   "rname"  "strand" "pos"    "qwidth" "mapq"   "cigar" 
 [9] "mrnm"   "mpos"   "isize"  "tag"   
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>