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

In reb: Regional Expression Biases

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.

Author(s)

Karl J. Dykema, [e-mail] Kyle A. Furge, [e-mail]

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

reb documentation built on April 28, 2020, 8:35 p.m.