IyerAnnotated {Iyer517}R Documentation

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)

[Package Iyer517 version 1.2.0 Index]