Regions with a log2 ratio above this value are considered

Deletion Threshold: Threshold for copy number deletions. Regions

with a log2 ratio below the negative of this value are considered

Cap Values: Minimum and maximum cap values on analyzed data.

Regions with a log2 ratio greater than the cap are set to the cap

value; regions with a log2 ratio less than -cap value are set to

Broad Length Cutoff: Threshold used to distinguish broad from

focal events, given in units of fraction of chromosome arm.

Remove X-Chromosome: Flag indicating whether to remove data from

the X-chromosome before analysis. Allowed values= {1,0} (1: Remove

X-Chromosome, 0: Do not remove X-Chromosome.

Confidence Level: Confidence level used to calculate the region

Join Segment Size: Smallest number of markers to allow in segments

from the segmented data. Segments that contain fewer than this number

of markers are joined to the neighboring segment that is closest

Arm Level Peel Off: Flag set to enable arm-level peel-off of events

during peak definition. The arm-level peel-off enhancement to the

arbitrated peel-off method assigns all events in the same chromosome

arm of the same sample to a single peak. It is useful when peaks are

split by noise or chromothripsis. Allowed values= {1,0} (1: Use arm

level peel off, 0: Use normal arbitrated peel-off).

Maximum Sample Segments: Maximum number of segments allowed for a

sample in the input data. Samples with more segments than this

threshold are excluded from the analysis.

Gene GISTIC: When enabled (value = 1), this option

causes GISTIC to analyze deletions using genes instead of array

markers to locate the lesion. In this mode, the copy number

assigned to a gene is the lowest copy number among the markers

List of inputs used for this run of GISTIC2. All files listed should be included in the archived results.

<span class="parameter">Arm Level Peel Off</span>

First 10 out of 110 Input Tumor Samples.

Segmented copy number profiles in the input data

The all lesions file summarizes the results from the GISTIC run. It contains data