Sample RNA-Seq Counts data

Description

A collection of counts datasets from Illumina Human Bodymap 2.0, one sample each for adipose, blood, heart and skeletal_muscle. Four technical replicates are created by downsampling the original Illumina data. Alignment was performed by Ensembl, so the source of this dataset is ftp://ftp.ensembl.org/pub/release-70/bam/homo_sapiens/genebuild . Each of the four Human Bodymap samples are downsampled four times. Read counts are collected with Bedtools CoverageBed and a RefSeq exon annotation.

Usage

data(IlluminaBodymap)

Format

A data frame with 37653 observations on the following 16 variables.

adipose.1

Illumina Human Bodymap 2 'Adipose' sample, downsampled to one-third.

adipose.2

Illumina Human Bodymap 2 'Adipose' sample, downsampled to one-third.

adipose.3

Illumina Human Bodymap 2 'Adipose' sample, downsampled to one-third.

adipose.4

Illumina Human Bodymap 2 'Adipose' sample, downsampled to one-third.

blood.1

Illumina Human Bodymap 2 'Blood' sample, downsampled to one-third.

blood.2

Illumina Human Bodymap 2 'Blood' sample, downsampled to one-third.

blood.3

Illumina Human Bodymap 2 'Blood' sample, downsampled to one-third.

blood.4

Illumina Human Bodymap 2 'Blood' sample, downsampled to one-third.

heart.1

Illumina Human Bodymap 2 'Heart' sample, downsampled to one-third.

heart.2

Illumina Human Bodymap 2 'Heart' sample, downsampled to one-third.

heart.3

Illumina Human Bodymap 2 'Heart' sample, downsampled to one-third.

heart.4

Illumina Human Bodymap 2 'Heart' sample, downsampled to one-third.

skeletal_muscle.1

Illumina Human Bodymap 2 'Skeletal Muscle' sample, downsampled to one-third.

skeletal_muscle.2

Illumina Human Bodymap 2 'Skeletal Muscle' sample, downsampled to one-third.

skeletal_muscle.3

Illumina Human Bodymap 2 'Skeletal Muscle' sample, downsampled to one-third.

skeletal_muscle.4

Illumina Human Bodymap 2 'Skeletal Muscle' sample, downsampled to one-third.

Value

A numeric matrix of read-counts from RNA-Seq, measured at transcripts by coverageBed.

Source

http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-513/

References

Illumina Human Bodymap 2.0. Ensembl etc.

Examples

data(IlluminaBodymap)
head(IlluminaBodymap,30)

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 '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
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> library(rgsepd)
Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
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


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: GenomeInfoDb
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: goseq
Loading required package: BiasedUrn
Loading required package: geneLenDataBase


Loading R/GSEPD 1.4.2
Building human gene name caches
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/rgsepd/IlluminaBodymap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: IlluminaBodymap
> ### Title: Sample RNA-Seq Counts data
> ### Aliases: IlluminaBodymap
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(IlluminaBodymap)
> head(IlluminaBodymap,30)
          adipose.1 adipose.2 adipose.3 adipose.4 blood.1 blood.2 blood.3
NM_000014     91717     91406     91667     91788     290     310     300
NM_000015         7         7         7         0       0       0       0
NM_000016      1395      1410      1505      1368    2592    2532    2681
NM_000017      1400      1439      1393      1334     460     449     507
NM_000018      9505      9432      9217      9780    4432    4466    4465
NM_000019      5609      5580      5707      5622    1530    1557    1565
NM_000020      5961      5625      5774      5862      98      74      96
NM_000021      3935      4092      3931      3964   12021   12010   12357
NM_000022       335       267       292       286     723     880     844
NM_000023       103       108        97        85      16      12      20
NM_000024      2488      2608      2726      2579    3478    3528    3270
NM_000025         0         0         0         0       0       0       0
NM_000026      1182      1174      1148      1168    2806    2676    2699
NM_000027       455       460       417       500    1475    1531    1465
NM_000028      1379      1564      1442      1433    2683    2721    2581
NM_000029      1166      1300      1278      1254       0       0       0
NM_000030         2         5         1         3       0       0       0
NM_000031      1336      1217      1264      1279    2151    2304    2292
NM_000032       479       442       511       537      13       5      13
NM_000033      1860      1931      1911      1803    1367    1295    1355
NM_000034     23007     23089     22909     23141   32509   32004   32363
NM_000035        13        12        19        20      11       7       6
NM_000036         0         0         0         0       0       0       0
NM_000037       149       114       136       113     431     455     407
NM_000038      2558      2477      2449      2502    6338    6271    6365
NM_000039        12        21         9        12      19      14      18
NM_000040        27        31        26        29       0       0       0
NM_000041      6865      6885      6972      6782       4       8       4
NM_000042         0         4         4         0       0       0       0
NM_000043       342       337       330       316    2686    2781    2626
          blood.4 heart.1 heart.2 heart.3 heart.4 skeletal_muscle.1
NM_000014     283   67285   66471   67355   67318             15609
NM_000015       0       3       3       8       3                 0
NM_000016    2491   15851   15994   15612   16046              2255
NM_000017     458    1992    1948    1939    1956              2759
NM_000018    4547   33252   33777   34008   33285             15478
NM_000019    1376   16616   16564   16696   16357             11988
NM_000020     111    1658    1532    1615    1600               497
NM_000021   12081    1570    1690    1776    1668              2009
NM_000022     895     144     150     144     147                75
NM_000023      24    1463    1433    1315    1388             13083
NM_000024    3459     338     398     358     330               325
NM_000025       0       8       0       4       2                 0
NM_000026    2777    1716    1734    1667    1616              7589
NM_000027    1478     376     288     361     351               108
NM_000028    2593    7910    7919    7712    7955              6610
NM_000029       0    5275    5189    5302    5136              3079
NM_000030       0       0       0       0       0                 0
NM_000031    2178    2702    2765    2859    2765               977
NM_000032       6      16      20       7      24                 8
NM_000033    1336     452     512     425     429              1547
NM_000034   32645   52469   52524   52855   52245            189075
NM_000035       9      45      43      44      48                 0
NM_000036       0       2       0       2       0             18654
NM_000037     426    2566    2580    2516    2633               946
NM_000038    6029    3984    4057    3916    4109              4263
NM_000039      17    1497    1497    1460    1502                 4
NM_000040       0       0       0       0       4                 0
NM_000041       0     627     585     549     575               469
NM_000042       0       0       0       0       0                 0
NM_000043    2723     249     217     280     196               140
          skeletal_muscle.2 skeletal_muscle.3 skeletal_muscle.4
NM_000014             15273             15573             15880
NM_000015                 0                 0                 0
NM_000016              2245              2362              2410
NM_000017              2887              2942              2989
NM_000018             15481             15478             15534
NM_000019             12108             12095             11758
NM_000020               475               496               449
NM_000021              1913              2067              2022
NM_000022                63                80                64
NM_000023             12502             12756             12943
NM_000024               354               301               354
NM_000025                 0                 0                 0
NM_000026              7724              7772              7759
NM_000027               206               174               168
NM_000028              6719              6641              6610
NM_000029              2854              2655              2853
NM_000030                 0                 0                 0
NM_000031              1061               995              1047
NM_000032                20                24                 8
NM_000033              1567              1455              1488
NM_000034            189006            189336            189087
NM_000035                 0                 0                 0
NM_000036             18722             18338             18733
NM_000037              1025              1104              1077
NM_000038              4233              4447              4582
NM_000039                12                 8                12
NM_000040                 0                 0                 0
NM_000041               457               511               491
NM_000042                 5                 5                 5
NM_000043               148               122               136
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>