export_gistic: Export GISTIC-compatible results
In sean-cho/Epicopy: Get CNV information from 450K array

Description Usage Arguments Details Value See Also Examples

View source: R/export_gistic.R

Parses the CNA result from LRRtoCNA and writes a segment file and marker file for input into GISTIC 2.0.

1 2	export_gistic(input, output_dir = NULL, filterbycount = TRUE, min_probes = 50, segfile_name = NULL, markerfile_name = NULL)

`input`	Result from `LRRtoCNA`.
`output_dir`	Output directory.
`filterbycount`	Logical. Recommended. Should the output segment file be filtered for having at least `min_probes` number of probes in the segment.
`min_probes`	Number of probes to filter against.
`segfile_name`	Name of the output segment file. NULL prints segmentation_output.
`markerfile_name`	Name of the output marker file. NULL prints marker_file.

export_gistic Exports gistic inputs.

Argument min_probes restricts segments to a certain number of probes or more if filterbycount is TRUE. Writes two output files, segmentation_output and marker_file which are the .seg and marker file inputs required for GISTIC 2.0.

Exports segmented data into GISTIC2 formatted input files.

preprocessFunnorm RGChannelSet-class

# Load included sample segmentation data
data(data_vignette)
# Export gistic files (defaults to local directory)
export_gistic(epi_seg, filterbycount = TRUE, min_probes = 50)