cnvkit_depth2igv: Write CNVkit cnr to wig
In pdiakumis/rock: Rocking R at UMCCR

Description Usage Arguments Value Examples

Reads the cnvkit.cnr file output by CNVkit and outputs its depth column into a wiggle file for easy viewing in IGV.

1	cnvkit_depth2igv(cnr, out_file = NULL, track_name = "val", col = "lightblue")

`cnr`	Path to CNVkit's `cnvkit.cnr` file, with `chromosome`, `start`, `end`, `gene`, `log2`, `depth` and `weight` columns.
`out_file`	Path to write output to. Needs to have a `wig` suffix.
`track_name`	Name of track to appear in IGV (default: "val").
`col`	Colour name for the bars (default: lightblue).

Invisible list with the modified cnr file and the track header.

## Not run: 
cnr <- system.file("extdata", "HCC2218-cnvkit_chr22_1K.cnr", package = "pebbles")
cnvkit_depth2igv(cnr, out_file = "HCC2218.cov.wig", track_name = "HCC2218_coverage", col = "orange")

## End(Not run)