Module contents¶
SNPknock module¶
knockoffDMC |
Class for knockoffs of a discrete Markov chain. |
knockoffDMC.sample(self, X) |
Sample a knockoff copy of each row of X. |
knockoffHMM |
Class for knockoffs of a hidden Markov model. |
knockoffHMM.sample(self, X) |
Samples a knockoff copy of each row of X. |
knockoffGenotypes |
Class for knockoffs of a hidden Markov model. |
knockoffGenotypes.sample(self, X) |
Samples a knockoff copy of each row of X. |
knockoffHaplotypes |
Class for knockoffs of a hidden Markov model. |
knockoffHaplotypes.sample(self, X) |
Samples a knockoff copy of each row of X. |
SNPknock.fastphase submodule¶
fastphase.writeXtoInp(X, out_file[, phased]) |
Convert the genotype data matrix X (consisting of 0,1 and 2’s) into the fastPhase input format and saves it to a text file. |
fastphase.runFastPhase(X_file, out_path[, …]) |
This function calls fastPhase to fit an HMM to the genotype data. |
fastphase.loadHMM(r_file, alpha_file, …[, …]) |
Load the parameter estimates obtained by fastPhase and assembles the HMM model for the genotype data. |
SNPknock.models submodule¶
models.DMC(pInit, Q) |
Discrete Markov chain model. |
models.DMC.sample([n]) |
Sample the observations from their marginal distribution. |
models.HMM(pInit, Q, pEmit) |
Hidden Markov model with a discrete emission distribution. |
models.HMM.sample([n]) |
Sample the n observations of the hidden Markov model. |