exportGRanges: Export GRanges object in a specified format
In yueli-compbio/RIPSeeker: RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments

Description Usage Arguments Value Note Author(s) References See Also Examples

A wrapper function of export with additional support for exporting tab-delimted format with no re-arrangement of the original GRanges output.

1	exportGRanges(gRanges, outfile, exportFormat)

`gRanges`	`GRanges` object to export.
`outfile`	File path for output.
`exportFormat`	Desirable format including "txt" and other formats specified in `export`.

Output the text to the file stream defined in outfile.

The function is used in ripSeek to export desired format and can be used as general purpose function.

Yue Li

Michael Lawrence, Vince Carey and Robert Gentleman. rtracklayer: R interface to genome browsers and their annotation tracks. R package version 1.16.3.

export

if(interactive()) { # need permission to write to the current dir
gr <-
    GRanges(seqnames =
            Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
            ranges =
            IRanges(1:10, width = 10:1, names = head(letters,10)),
            strand =
            Rle(strand(c("-", "+", "*", "+", "-")),
                c(1, 2, 2, 3, 2)),
            score = 1:10,
            GC = seq(1, 0, length=10))

	outfile <- paste(getwd(), "/gr.txt", sep="/")

	exportGRanges(gr, outfile=outfile, exportFormat="txt")
}