The second section can be identified the rows in which column 9 reads 'Actual

Copy Change Given.'  The second section exactly reproduces the first section,

except that here the actual changes in copy number are provided rather than

The final section is similar to the first section, except that here only broad

events are included. A 1 in the samples columns (columns 10+) indicates that

the median copy number of the sample across the entire significant region

exceeded the threshold given in column 9. That is, it indicates whether the

sample had a geographically extended event, rather than a focal amplification

or deletion covering little more than the peak region.

All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level)

The amp genes file contains one column for each amplification peak identified

in the GISTIC analysis.  The first four rows are:

These rows identify the lesion in the same way as the all lesions file.

The remaining rows list the genes contained in each wide peak.  For peaks

that contain no genes, the nearest gene is listed in brackets.

Amplification Genes File (amp_genes.conf_##.txt, where ## is the confidence level)

The del genes file contains one column for each deletion peak identified in

the GISTIC analysis. The file format for the del genes file is identical to

Deletion Genes File (del_genes.conf_##.txt, where ## is the confidence level)

The scores file lists the Q values [presented as -log10(q)], G scores,

average amplitudes among aberrant samples, and frequency of aberration,

across the genome for both amplifications and deletions. The scores file is

viewable with the Genepattern SNPViewer module and may be imported into the

The segmented copy number is a pdf file containing a colormap image of the

segmented copy number profiles in the input data.

Segmented Copy Number (raw_copy_number.{fig|pdf|png} )

The amplification pdf is a plot of the G scores (top) and Q values (bottom)

with respect to amplifications for all markers over the entire region

Amplification Score GISTIC plot (amp_qplot.{fig|pdf|png|v2.pdf})