Call function: How to interpret log2(absolute copy number integers of a segment)

[etal]

Call function: How to interpret log2(absolute copy number integers of a segment)

[etal]

The copy numbers are relative to the specified ploidy (default 2) -- they are still log2 ratios with the same interpretation as the segmentation output (.cns). This is so that you can plot the .absoluteCN.cns file with the scatter/heatmap/diagram commands the same way you would with the original .cns file. The call command just rounds the segment means to what they would be if the true copy number were an integer.

To get the absolute integers in a human-readable form, try:

cnvkit.py export bed sampleName.absoluteCN.cns --show-neutral

The thresholds work like this (see cnvlib.call.absolute_threshold ):

if log2 <= -4.3: CN=0
if log2 <= -1: CN=1
if log2 <= 0: CN=2
if log2 <= 0.6: CN=3
...

So the germline thresholds, rounding to the nearest log2(integer), could be calculated like:

> log2( (0:4 + .5 ) / 2)
[1] -2.0000000 -0.4150375  0.3219281  0.8073549  1.1699250

Sorry for the confusion. I'll update the docs.

[jperales]

Thank you very much! It is clear now.
Javier