bedval2igv: Export BED values for IGV Viewing
In umccr/rock: Rocking R at UMCCR

Description Usage Arguments Value Examples

Given a BED-like file with chromosome, start, end and value columns, export a properly formatted file for viewing the values as a scatter plot in IGV. Note that start needs to be equal to end, since we're looking at specific SNPs, not segments.

1	bedval2igv(bed, out_file = NULL, track_name = "val", col = "purple")

`bed`	BED file with `chrom`, `start`, `end` and `value` columns.
`out_file`	Path to write output to. Needs to have an `igv` suffix.
`track_name`	Name of track to appear in IGV (default: "val").
`col`	Colour name for the points (default: blue).

Invisible list with the modified BED file and the track header, where:

chrom: chromosome
start: start coordinate
end: end coordinate
name: just an ID for the row (chrom:start-end)
val: value
header: track information

## Not run: 
bed <- system.file("extdata", "HCC2218_baf.tsv", package = "pebbles")
bedval2igv(bed, out_file = "~/Desktop/tmp/baf1.igv", track_name = "hcc2218_baf", col = "red")

## End(Not run)