Bug fix in background signature estimation

[yihming]

Issue

When estimating background signature given a sparse count matrix, in pegasus.cylib.calc_sig_background_sparse function, the calculation ignores zero entries of the matrix, while their centered expression should be considered because the gene mean expressions are likely non-zero.

However, if given a dense count matrix, the calculation does not have this issue since it uses a different Cython function pegasus.cylib.calc_sig_background_dense.

Solution

Include all entries during the calculation, with tricks to speed up.

Other improvement

Add standardize parameter to calc_signature_score function to allow return non-standardized signature scores. By default, standardize the scores.