supplemental data extract on RNA seq results in yeast

Description

supplemental data extract on RNA seq results in yeast

Usage

data(leeRPKM)

Format

A data frame with 6291 observations on the following 16 variables.

chr

a numeric vector

strand

a numeric vector

start

a numeric vector

end

a numeric vector

name

a factor with levels LSR1 NME1 YAL001C YAL002W YAL003W ...

feature

a factor with levels CDS CDS_unchar snRNA snoRNA

orf_classification

a factor with levels Uncharacterized Verified silenced_gene3AVerified

gene

a factor with levels AAC1 AAC3 AAD10 AAD14 AAD15 AAD16 AAD3 AAD4 ...

wt.reads

a numeric vector

rrp.reads

a numeric vector

ski.reads

a numeric vector

xrn.reads

a numeric vector

wt.rpkm

a numeric vector

rrp.rpkm

a numeric vector

ski.rpkm

a numeric vector

xrn.rpkm

a numeric vector

Source

imported from supplemental data

References

Lee et al PLOS genetics December 2008 ; Volume 4 ; Issue 12 ; e1000299

Examples

data(leeRPKM)
leeRPKM[1:5,]

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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> library(leeBamViews)
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: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: BSgenome
Loading required package: rtracklayer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/leeBamViews/leeRPKM.Rd_%03d_medium.png", width=480, height=480)
> ### Name: leeRPKM
> ### Title: supplemental data extract on RNA seq results in yeast
> ### Aliases: leeRPKM
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(leeRPKM)
> leeRPKM[1:5,]
  chr strand start   end      name    feature orf_classification gene wt.reads
1   1     -1  1807  2169   YAL068C CDS_unchar    Uncharacterized PAU8        0
2   1      1  2480  2707 YAL067W-A CDS_unchar    Uncharacterized <NA>        0
3   1     -1  7236  9017   YAL067C        CDS           Verified SEO1        6
4   1     -1 11566 11952   YAL065C CDS_unchar    Uncharacterized <NA>        6
5   1      1 12047 12427 YAL064W-B CDS_unchar    Uncharacterized <NA>        2
  rrp.reads ski.reads xrn.reads wt.rpkm rrp.rpkm ski.rpkm xrn.rpkm
1         0         0         0 0.00000  0.00000  0.00000  0.00000
2         0         0         0 0.00000  0.00000  0.00000  0.00000
3        94        10       132 0.23874  3.64399  0.37477  6.91370
4        14        10        13 1.09933  2.49905  1.72569  3.13528
5         2         0         5 0.37221  0.36263  0.00000  1.22487
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>