PeteHaitch / methsim / 83

Builds Branch Commit Type Ran Committer Via Coverage
83 master Fix simulate2,SimualteBSParam2-method. - Pass entire SimulateMethylome2 object, not just rowRanges. - Don't SIMPLIFY or USE.NAMES in bpmapply(). push PeteHaitch travis-ci pending completion   set done
82 master Add simulate2,SimulateBSParam2-method. Add .simulatez() to simulate reads as part of simulate2,SimulateBSParam2-method. push PeteHaitch travis-ci pending completion   set done
80 master Update argument names to .computeP() to better reflect their value. Delete already commented out code in .computeP() that is not required. push PeteHaitch travis-ci pending completion   set done
79 master Re-write .computeP() to avoid the need for the seqnames_one_tuples argument (also requires changes to the lor_by_pairs argument). push PeteHaitch travis-ci pending completion   set done
78 master Add SimulateBSParam2 class. push PeteHaitch travis-ci pending completion   set done
76 master Add seqlevels argument to simulate,SimulateBSParam-method. Re-write .sampleZ() to return an Rcpp::IntegerVector rather than Rcpp::List, which in turn simplifies (and speeds up) simulate,SimulateBSParam-method. push PeteHaitch travis-ci pending completion   set done
75 master Experiment with a new version of .sampleZ(), .sampleZvec(). push PeteHaitch travis-ci pending completion   set done
74 master Comment on order of columns in P. push PeteHaitch travis-ci pending completion   set done
73 master Fix colnames of P push PeteHaitch travis-ci pending completion   set done
72 master Switch orientation of P to be compatible with SummarizedExperiment. Change return type of .computeP() to a Rcpp::NumericMatrix. Add dummy column names to P to be compatible with SummarizedExperiment. push PeteHaitch travis-ci pending completion   set done
71 master Missing default value for nsim in simulate2(). push PeteHaitch travis-ci pending completion   set done
70 master Fix bug when creating 2-tuples for a seqlevel with insufficient 1-tuples. push PeteHaitch travis-ci pending completion   set done
69 master Typos push PeteHaitch travis-ci pending completion   set done
68 master Re-jig how seqlevels argument of simulate,SimulateMethylomeParam-method and simulate2,SimulateMethylomeParam-method works. Should improve performance since only those seqlevels will be used when creating 1-tuples and 2-tuples. push PeteHaitch travis-ci pending completion   set done
67 master Add SimulateMethylome2 class, a modified version of the SimualteMethylome2 class. Specifically, it only stores the transition probabilities, (P), rather than the simulated 'true' methylome (Z, W). Wrote a simulate2,SimulateMethylome2-method, to co... push PeteHaitch travis-ci pending completion   set done