CNA CN file (.cn) is a tab-delimited text file that contains copy number data. The CN file format is described on the GenePattern web site: http://www.broadinstitute.org/cancer/software/genepattern/gp_guides/file-formats/sections/cn. Zero-based index: Physical positions are identified using a zero-based index. Display settings: To modify IGV's default display settings for the CN data, include a track line in the file. Example: mynah.sorted.cn Does IGV assume log2(ratio) or absolute values for copy number?IGV looks for the presence of negative numbers. If it finds them, it assumes that the data is log2(tumor/normal). If it does not find negative numbers, it assumes that the values are absolute, with 2 as the center. These assumptions are used to set the heatmap legend; the legend can, however, be changed manually under the View> Color Legends. Instructions are found in the Color Legends section of the user guide. For data with negative numbers, IGV defaults to a blue-to-red scale that corresponds to copy numbers from -1.5 to 1.5. Both deletions and amplifications can have continuous valued numbers represented by shading. |