Metadata table for the included sample data

Description

The metadata table required to inform GSEPD of the sample/condition and abbreviated names for each column of the included 'counts' dataset. You should mirror this table's structure for your dataset.

Usage

data(IlluminaBodymapMeta)

Format

A data frame with 16 observations on the following 3 variables.

Sample

A vector of the column names in your counts table, for the included sample data, it's four tissue types repeated four times each. For your data this must correspond to the column labels in the counts table.

Condition

The sample categorizations for use in differential expression, this should also be a vector the same length as the number of columns in your counts table. Here we have 'A' for each Adipose, 'B' for each muscle type, and 'C' for the blood samples.

SHORTNAME

Abbreviated names for each sample to appear in plots.

Value

A dataframe of sample identifiers for the rgsepd::IlluminaBodymap matrix.

Examples

data(IlluminaBodymapMeta)
str(IlluminaBodymapMeta) 

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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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/IlluminaBodymapMeta.Rd_%03d_medium.png", width=480, height=480)
> ### Name: IlluminaBodymapMeta
> ### Title: Metadata table for the included sample data
> ### Aliases: IlluminaBodymapMeta
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(IlluminaBodymapMeta)
> str(IlluminaBodymapMeta) 
'data.frame':	16 obs. of  3 variables:
 $ Sample   : Factor w/ 16 levels "adipose.1","adipose.2",..: 1 2 3 4 5 6 7 8 9 10 ...
 $ Condition: Factor w/ 3 levels "A","B","C": 1 1 1 1 3 3 3 3 2 2 ...
 $ SHORTNAME: Factor w/ 16 levels "AD1","AD2","AD3",..: 1 2 3 4 5 6 7 8 9 10 ...
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>