CNA-seq / Plot copy number profiles

Description

Plot copy number profiles of individual arrays from called aCGH data.

Parameters

• Samples to be plotted (1...n) [1]
• Chromosomes to be plotted (0...25) [0]

Details

Original log ratios are shown in black, segmented values in brown, probabilities of losses in red (right scale), and probabilities of gains in blue (inverted right scale)

Output

aCGH profile of individual sample(s).

References

QDNAseq:
Scheinin et al. (2014) DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Res In Press.

CGHcall
Wiel et al. (2007) CGHcall: calling aberrations for array CGH tumor profiles. Bioinformatics 23: 892-894