Package 'Iyer517'

query genbank for an EST accession id

Description

extends the get.dna function of E Paradis CRAN package "ape"

Usage

get.dna2(access.nb)

Arguments

access.nb

an EST accession id

Details

queries ncbi

Value

a vector of nucleotide codes

Note

try ape::get.dna if this fails

Author(s)

VJ Carey <[email protected]>

See Also

ape::get.dna

Examples

if (interactive())
{
data(IyerAnnotated)
get.dna2(IyerAnnotated$GB[1])
}

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exprSet instance Iyer517, time series on transcriptional response of fibroblasts to serum

Description

an expression set for timed measurements of transcriptional response of fibroblasts to serum in presence or absence of cycloheximide

Slots

exprs:

Object of class matrix, value: 517 x 19 expression levels (normed to 1 at time 0)

se.exprs:

Object of class matrix, value: absent

description:

Object of class MIAME, value: string

annotation:

Object of class character, value: ”

notes:

Object of class character, value: ”

phenoData:

Object of class phenoData, value: data frame with info on timing

class:

Object of class character, value: 'exprSet'

References

Iyer et al 1999 Science v283 83-87

Examples

data(Iyer517)
show(Iyer517)
plot(apply(exprs(Iyer517)[1:100,1:13],2,mean),main="Cluster A",
xlab="index in time seq", ylab="ratio to time 0", log="y")

---

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)

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