writeGFF3: Output of a GFF compliant table describing the enhanced and diminished chromosomal bands.

Description

This function writes out a GFF compliant tab delimited file for intergration with genome browsers.

Usage

writeGFF3(cset, genome, chr, file.prefix = "temp.gff", organism = NULL)

Arguments

cset

expression set containing cytogenetic predictions, see reb

genome

chromLocation object containing annotation information

chr

chromosome to examine

file.prefix

character string - name of the output file, defaults to "temp.gff"

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

writeGFF3 returns an invisible list of character vectors.

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

Examples

Run this code



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)
gffmat <- writeGFF3(colo.eset,ucsf.chr,"14",NULL)
gffmat[1:4,]