\HeaderA{agMAP}{Map between Manufacturer Identifiers and cytogenetic maps/bands}{agMAP}
\keyword{datasets}{agMAP}
\begin{Description}\relax
agMAP is an R environment that provides mappings between
manufacturer ids and cytoband locations.
\end{Description}
\begin{Details}\relax
Each manufacturer id is mapped to a vector of cytoband locations. The
vector length may be one or longer, if there are multiple reported
chromosomal locations for a given gene. An \code{NA} is reported for
any manufacturer ids that cannot be mapped to a cytoband at this time.

Cytogenetic bands for most higher organisms are labeled p1, p2, p3,
q1, q2, q3 (p and q are the p and q arms), etc., counting from the
centromere out toward the telomeres. At higher resolutions, sub-bands
can be seen within the bands. The sub-bands are also numbered from the
centromere out toward the telomere. Thus, a label of 7q31.2 indicates
that the band is on chromosome 7, q arm, band 3, sub-band 1, and
sub-sub-band 2.   

The physical location of each band on a chromosome can be obtained
from another environment named "organism"CYTOLOC in a separate data
package for human(humanCHRLOC), mouse(mouseCHRLOC), and rat(ratCHRLOC).  

Mappings were based on data provided by:

Entrez Gene:\url{http://gopher5/compbio/annotationSourceData/ftp.ncbi.nlm.nih.gov/gene/DATA/}. Built: Source data downloaded from Entrez Gene on Tue May 17 18:26:20 2005

Package built Tue May 17 18:29:49 2005
\end{Details}
\begin{References}\relax
\url{http://www.ncbi.nlm.nih.gov}
\end{References}
\begin{Examples}
\begin{ExampleCode}
    # Convert the environment to a list
    xx <- as.list(agMAP)
    # Remove probe ids that do not map to any cytoband
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
        # The cytobands for the first two elements of XX
        xx[1:2]
        # Get the first one
        xx[[1]]
    }
\end{ExampleCode}
\end{Examples}

