revish {reb}R Documentation

Creation of CGH (reverse in situ hybridization) style character strings

Description

This function returns a two lists of character strings. These two lists correspond to the enhanced and diminished chromosomal bands.

Usage

revish(cset, genome, chr, organism = NULL)

Arguments

cset expression set containing cytogenetic predictions, see reb
genome chromLocation object containing annotation information
chr chromosome to examine
organism if NULL, determination of the host organism will be retrieved from the organism slot of the chromLocation object. Otherwise "h", "r", or "m" can be used to specify human, rat, or mouse chromosome information

Value

enh list of enhanced bands on each individual sample
dim list of diminished bands on each individual sample

Author(s)

Karl J. Dykema, karl.dykema@vai.org Kyle A. Furge, kyle.furge@vai.org

References

Furge KA, Dykema KJ, Ho C, Chen X. Comparison of array-based comparative genomic hybridization with gene expression-based regional expression biases to identify genetic abnormalities in hepatocellular carcinoma. BMC Genomics. 2005 May 9;6(1):67. PMID: 1588246

MCR eset data was obtained with permission. See PMID: 15377468

See Also

reb

Examples


data(idiogramExample)
ix <- abs(colo.eset) > .225
colo.eset[ix] <- NA
idiogram(colo.eset,ucsf.chr,"14",method="i",dlim=c(-1,1),col=.rwb)
revlist<- revish(colo.eset,ucsf.chr,"14")
str(revlist)


[Package reb version 1.16.0 Index]