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Outputs from CNAM Optimal Segmenting

10.4 Outputs from CNAM Optimal Segmenting

CNV Covariates Spreadsheet

The first one (or two) spreadsheet(s) created upon segmenting is a covariates spreadsheet(s). This spreadsheet contains the average log2 ratio value for each sample within each segment of markers. In this spreadsheet, the rows correspond to the samples, the columns correspond to the overall segments which have been determined, and the data are the average log2 ratio values. The spreadsheet created also has the original marker map applied. There are two covariate spreadsheet variants, one or both can be output from the segmenting results and are described below.

First column of each segment

In this variant, each column is identified by the chromosome number and the beginning marker of each segment (see Figure 82). The markers are identified by chromosome position. A new column is created every time there is a new cut-point over all of the samples. This creates common segments for all samples, although for a particular sample there may be more columns than there are cut-points. In the case where a new column is introduced but a cut-point was not found for that sample, the CNV segment mean is repeated for all columns in a segment. A new segment mean only occurs for each new segment for each sample. This spreadsheet is ideal for association testing as the Bonferroni multiple testing correction is reduced.

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One column per marker

In this variant, each column is identified by the marker name (see Figure 83). A new column is created for every marker present in the original segmented spreadsheet. The mean segment value is repeated for every marker in each segment found, and only changes when cut-points are reached. This spreadsheet is ideal to use for plotting as there is a value for every marker, better demonstrating copy number amplifications and deletions.

CNV Segment List Spreadsheet

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The third spreadsheet created upon segmenting is a list of CNV segments means (see Figure 84). This spreadsheet contains columns for the chromosome name, segment base start position, segment base end position, segment mean, the number of markers in the segment, the segment column start index, and the segment column end index. Spreadsheet rows correspond to segments for each sample. If a sample has 1,000 segments, then there will be 1,000 rows for the sample before the next sample starts.

Segment Run Log

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The details of the segment run log displayed while segmenting, is saved and output in the Segment Run Log for future reference (see Figure 85). This log details if the maximum number of segments found was reached and if the window size was doubled due to avoid potential edge issues with the segmenting algorithm.

Wiggle Track (WIG) File

If you chose to output WIG files they will be saved in the directory you selected.