1) How do I determine which samples exhibit which signatures?

There are two main ways for exploring which signature is present in which sample:

1) Use the samples method on the result of the identifySignatures step, e.g. samples(sigs). This will give you a matrix of the form 'sample' x 'signature'. 

2) Visualize the result with the plotSampleMap or plotSamples methods. The vignette gives a number of examples for this.