From 98d71a9f8b5d9e53025eba10eb47f38b6466f764 Mon Sep 17 00:00:00 2001 From: HannahVMeyer Date: Mon, 24 Aug 2020 13:13:35 -0400 Subject: [PATCH] Add cran-comments --- cran-comments.md | 47 +++++++++++++++++++---------------------------- 1 file changed, 19 insertions(+), 28 deletions(-) diff --git a/cran-comments.md b/cran-comments.md index 863549f..9ffa5be 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,35 +1,26 @@ -## Resubmission -# plinkQC 0.3.2 -## minor changes -* Add checks and tests in `evaluate_check_ancestry` for missing non-reference samples -[5c03971](https://github.com/meyer-lab/plinkQC/commit/5c03971b92341b5a8cb26a1d5f2e37d637f5cbd7) -* Clarified tutorials: - * R internal file.copy instead of systems `cp` command to make run on windows: [6c91ef3](https://github.com/meyer-lab/plinkQC/commit/6c91ef3368f601658967f88bc20db94a28307fce), - fixes [#26](https://github.com/meyer-lab/plinkQC/issues/26) - * Add additional filter for A->T, C->G variants as suggested in [#24](https://github.com/meyer-lab/plinkQC/issues/24); [11e0375](https://github.com/meyer-lab/plinkQC/commit/11e03756852215915310a836d2e73dbcedf12bfc) -* Fixed plotting issues in PCA plot of ancestry check: - * allow for supplying names of European reference population [ae09e64](https://github.com/meyer-lab/plinkQC/commit/ae09e64ee2eaeb8337b60b24b126a9c049d6315f) - * provide argument to specify number of populations per legend row [c7fe85d](https://github.com/meyer-lab/plinkQC/commit/c7fe85d555c256bf8be3843803ff1cc445f7898f) - * Ensure correct ordering of population colors when reference population is not HapMap [86275b7](https://github.com/meyer-lab/plinkQC/commit/86275b7c281835681f38ab16672db61c288cfed9) - -# plinkQC 0.3.1 -## minor changes - -* Fixed dead links in vignettes (caused by migration of repository): [da987d8](https://github.com/meyer-lab/plinkQC/commit/da987d8f225aa6aca0596b9c4f6a2484b102bdb6) -* Added note about chrY in Hapmap data (vignette): [e8afbb9](https://github.com/meyer-lab/plinkQC/commit/e8afbb9842ed9421461a8114ac0a00f7955cf0c0) -* Added note about recommended use of plink1.9 (vs 2.0): -[b69d3d7](https://github.com/meyer-lab/plinkQC/commit/b69d3d71d23e9b161176a635fcb2b5a2b524591f) - ## Test environments -* local R installation, R 4.0.0 -* ubuntu 16.04 (on travis-ci), R 4.0.0 +* local R installation, R 4.0.2 +* ubuntu 16.04 (on travis-ci), R 4.0.2 * win-builder (devel) ## R CMD check results 0 errors | 0 warnings | 1 note -## Comments -* This is a minor release -* Mostly updates to vignettes and documentation -* Some additional checks and tests on ancestry check +* This is a new release, addressing some minor bug fixes and adding some more +functionality. + +# plinkQC 0.3.3 +## major changes +* Output all IBD estimates in `run_check_relatedness` not just fail IBD +estimates [d009da90](https://github.com/meyer-lab/plinkQC/commit/d009da90434a83cb4867881e3772b518d17dc2dd) +* Add midp modifier for --hwe and --hardy as recommended on [plink hwe documentation](https://www.cog-genomics.org/plink/1.9/filter#hwe) and discussed in issue [#27](https://github.com/meyer-lab-cshl/plinkQC/issues/27); [43230a6c](https://github.com/meyer-lab/plinkQC/commit/43230a6ce5f079b46c85b1a7a526213177db1f1b) + +## minor changes +* Add checks in `cleanData` that can distinguish between miss-sepcified filters and non-failing samples [7432b1ee](https://github.com/meyer-lab/plinkQC/commit/7432b1ee880ad14c7a078f3a0379f7fdcff1684b); addresses issue [#31](https://github.com/meyer-lab-cshl/plinkQC/issues/31) +* Add checks and tests in `check_snp_missingness`, `check_maf` and `check_hwe` +in cases where all samples pass `perIndividualQC`. +[31ed6f65](https://github.com/meyer-lab/plinkQC/commit/31ed6f653902857a0a78ae723e786dd84d240b75); related to issue [#31](https://github.com/meyer-lab-cshl/plinkQC/issues/31) +* Add checks and tests in `evaluate_check_sex` and `evaluate_check_het_imiss` +for all passing samples and accordingly, no fail samples label in plot. +[d071a43](https://github.com/meyer-lab/plinkQC/commit/d071a4341b0d4c40220b42f81c412da4d320b8ec)