A function to generate an instantiation of a chromLocation class

Description

This function will take take the name of a data package and build a chromLocation object representing regions of the genomes.

Usage

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buildChromMap(dataPkg, regions)

Arguments

dataPkg

The name of the data package to be used (a.k.a generated by AnnBuilder or downloaded from Bioconductor web site

regions

a character vector of genome regions to be generated

Details

This function is related to the buildChromLocation function found in the 'annotate' library. However, this function can be used to build specialized chromLocation objects based on gene mapping information. For example, a chromLocation object can be build specifically for human chromosome 1 by supplying chromosomal band information, such as c("1p1", "1p2", "1p3", "1q1", "1q2", "1q3", "1q4"). Genes that map to these regions are isolated and a chromLocation object is returned. Note that genes are isolated by 'grep'ing genome mapping information. Therefore the number of genes that are able to placed into a defined genetic region (i.e. 1q4) is dependent on the quality of the mapping information in the annotation data source.

Unfortunately, not too many pre-built annotation packages are available for spotted arrays off the Bioconductor Metadata web set. Use AnnBuilder to make one or get one from your core.

Value

A 'chromLocation' object representing the specified genomic regions and annotation data source

Author(s)

Kyle A. Furge <kyle.furge@vai.org

See Also

buildChromLocation

Examples

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## 
## NOTE: This requires an annotation package to work, it is provided for info only.
##       

#if (require(hu6800)) {

#  library(Biobase)
#  library(annotate)

  ## Build a specific chrom arm

#  chr1q <- buildChromMap("hu6800",c("1q1","1q2","1q3","1q4"))

  ## Build human data based on chrom arms

#  data(Hs.arms) 
#  map <- buildChromMap("hu6800",Hs.arms)
#}