writeGFF3 {reb} | R Documentation |
This function writes out a GFF compliant tab delimited file for intergration with genome browsers.
writeGFF3(cset, genome, chr, file.prefix = "temp.gff", organism = NULL)
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 |
writeGFF3
returns an invisible list of character vectors.
Karl J. Dykema, karl.dykema@vai.org Kyle A. Furge, kyle.furge@vai.org
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
data(idiogramExample) ix <- abs(colo.eset@exprs) > .225 colo.eset@exprs[ix] <- NA idiogram(colo.eset@exprs,ucsf.chr,"14",method="i",dlim=c(-1,1),col=.rwb) gffmat <- writeGFF3(colo.eset@exprs,ucsf.chr,"14",NULL) gffmat[1:4,]