lcdblib.expression package

Submodules

lcdblib.expression.expression_utils module

lcdblib.expression.expression_utils.zFPKM(log_fpkm, resolution=100)

Should we consider a gene “expressed” or not?

Implements algorithm from Hart et al 2013 (DOI:10.1186/1471-2164-14-778). In that paper, using human data they conclude that zFPKM < -3 is a reasonable cutoff since at that point, the frequency of repressive chromatin marks outweighs active marks.

Parameters:

• log_fpkm (array-like) – FPKM (or TPM) on a log scale
• resolution (int) – Use this many evenly-spaced points between min and max log_fpkm

Returns:

xi: basis over which the kde was evaluated yi: the kde mu: maximum of the kde U: mean of log_fpkm values > mu sigma: std of the fitted half-gaussian zfpkm: z-transformed FPKM

Return type:

Dictionary of values as follows

Module contents