| 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) > .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,]