sartorlab / methylSig / 240

Builds Branch Commit Type Ran Committer Via Coverage
240 Bioc_3_10 Issue #37: Add filter_loci_by_location() * Function removes loci from bs that are in gr. * This function will be used in the SNP removal function once the SNPs are arranged into a GRanges. * Added some testing data in data-raw/03-create_internal_... push rcavalcante travis-ci pending completion   set done
239 Bioc_3_10 Issue #34: Add diff_binomial() * Variable naming conventions are aligned with diff_methylsig() in replacing 'creads' and 'treads' with 'meth_reads' and 'unmeth_reads', respectively. Also variables ending in 1/2 are replaced with control/case, res... push rcavalcante travis-ci pending completion   set done
238 Bioc_3_10 Issue #36: Stable diff_dss_fit() and diff_dss_test() * Implemented methylation recovery via factors in a factor vector from the design matrix as well as via percentiles in a numeric vector from the design matrix. Took a more direct approach to st... push rcavalcante travis-ci pending completion   set done
237 Bioc_3_10 WIP: Issue #36: Add guardrails to diff_dss_test() push rcavalcante travis-ci pending completion   set done
236 Bioc_3_10 WIP: Issue #36: Add diff_dss_fit() and diff_dss_test() In line with other testing packages, split the fit and test functions. the _fit() function will be a direct wrapper of DSS::DMLfit.multiFactor(), and the test function will have some addition... push rcavalcante travis-ci pending completion   set done
235 Bioc_3_10 Issue #35: Stable diff_methylsig() * Also added comment lines to other functions for improved readability. * Currently not testing output of diff_methylsig() because not sure what to test. Will circle back to this prior to release. push rcavalcante travis-ci pending completion   set done
234 Bioc_3_10 WIP Issue #35: Improve diff_methylsig() * Improve documentation * Fix needless S4Vectors:: usage * Remove use of metadata for now push rcavalcante travis-ci pending completion   set done