reb (version 1.50.0)

revish: 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

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)