Description Usage Arguments Details Value Examples
Function for counting altered base segments
1 | countingBaseSegments(cnvData, segmentMean = 0.2, numProbes = NA)
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cnvData |
dataframe containing following columns: Sample, Start, End, Num_Probes, Segment_Mean |
segmentMean |
numerical value for the minimum segment_mean cutoff/ threshold. Default is 0.2 |
numProbes |
Number of Probes |
The Altered Base Segment calculation takes all the CNV data for a single patient and first filters it for a segmentation mean of > 0.2 and, if specified, the minimum number of probes covering that area. Then, it calculates the sums of the lengths of each segment for a particular patient and outputs that.
Number\ of\ Altered\ Bases = ∑^{R}_{i = 1} d_i\ where\ |\bar{y}_{S_i}| ≥ 0.2
Number of Base segments for each unique sample
1 | countingBaseSegments(cnvData = maskCNV_BRCA)
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