Partly annotated version of Iyer517 data

Description

GenBank ids, LocusLink ids (where available) and GO tags (where available) for the 517 cDNAs in the dataset.

Usage

data(IyerAnnotated); data(Iyer517GO)

Format

Iyer517GO: An environment with keys given by the 'GB' identifiers of probes and values given by vectors of GO tags (named by evidence codes) obtained via locuslink mapping

IyerAnnotated: A data frame with 517 observations on the following 9 variables.

Iclust

a factor with levels N A B ... – the cluster groups A-J of the Iyer paper, with N for those rows that were not clustered

GB

a factor with levels AA001025 AA001722 ... accession numbers (often genbank) for probes

seqno

a numeric vector indicating the order of the cDNA in the Iyer report on clustering. (Elements 2:101 formed cluster A, etc.)

locusid

a numeric vector of locuslink ids, formed using AnnBuilder

GO1

a character vector of GO tags (there were up to five based on the LL:GO mapping available March 2003 – these should be ignored in favor of the new Iyer517GO environment

GO2

a character vector

GO3

a character vector

GO4

a character vector

GO5

a character vector

Details

Annotating this dataset is a good exercise for AnnBuilder. Many of the probes seem to have no annotation.

Source

http://genome-www.stanford.edu/serum/data.html

References

Iyer et al, Science v283: 83-87 (1999)

Examples

data(IyerAnnotated)
table(is.na(IyerAnnotated$GO1))
data(Iyer517GO)
get(ls(env=Iyer517GO)[1],env=Iyer517GO)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(Iyer517)
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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Iyer517/IyerAnnotated.Rd_%03d_medium.png", width=480, height=480)
> ### Name: IyerAnnotated
> ### Title: Partly annotated version of Iyer517 data
> ### Aliases: IyerAnnotated Iyer517GO
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(IyerAnnotated)
> table(is.na(IyerAnnotated$GO1))

FALSE  TRUE 
  211   306 
> data(Iyer517GO)
> get(ls(env=Iyer517GO)[1],env=Iyer517GO)
         TAS           NR 
"GO:0003714" "GO:0003700" 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>