diff --git a/src/htrsim/DESCRIPTION b/src/htrsim/DESCRIPTION index 305c99cc108fdef2876d7bfb20091fe3170a5625..a5ca29cf36ef2e37f87a7c189fbd1de514eba326 100644 --- a/src/htrsim/DESCRIPTION +++ b/src/htrsim/DESCRIPTION @@ -24,4 +24,8 @@ Imports: data.table, plyr, reshape2, - tidyr + tidyr, + S4Vectors, + readr, + testthat +Config/testthat/edition: 3 diff --git a/src/htrsim/NAMESPACE b/src/htrsim/NAMESPACE index 5958cecbc6d6929d2b1287758882773ec1b72daf..b6f56d78a61bdd832958ac75acd66437379e5e6c 100644 --- a/src/htrsim/NAMESPACE +++ b/src/htrsim/NAMESPACE @@ -2,6 +2,7 @@ export(estim.alpha) export(estim.mu) +export(estim.mu_beta) export(generate_counts) export(handle_except) export(htrsim) @@ -11,10 +12,12 @@ export(run.deseq) export(setup_countGener) import(BiocGenerics) import(DESeq2) +import(S4Vectors) import(data.table) import(dplyr) import(plyr) import(purrr) +import(readr) import(reshape2) import(stats) import(stringr) diff --git a/src/htrsim/devtools_history.R b/src/htrsim/devtools_history.R index 69ccee8903792230b5f92875c9ac458a73bb87d6..38b57d876b3f7dc9a71641af916eecdee46826d9 100644 --- a/src/htrsim/devtools_history.R +++ b/src/htrsim/devtools_history.R @@ -11,4 +11,8 @@ usethis::use_package("data.table") usethis::use_package("plyr") usethis::use_package("reshape2") usethis::use_package("tidyr") +usethis::use_package("S4Vectors") +usethis::use_package("readr") +usethis::use_package("testthat") +usethis::use_test("name") devtools::load_all() diff --git a/src/htrsim/inst/extdata/public_bioDesign.csv b/src/htrsim/inst/extdata/public_bioDesign.csv index a4e913ccbfee23c85aaf0d48f74a1d37aa57f58a..9c0ad939452866990ab5b5b497fdf4cdae622628 100644 --- a/src/htrsim/inst/extdata/public_bioDesign.csv +++ b/src/htrsim/inst/extdata/public_bioDesign.csv @@ -1,13 +1,13 @@ -sample;env;mutant;mutant_env -Msn2D_KCl_rep1;kcl;msn2D;msn2D_kcl -Msn2D_KCl_rep2;kcl;msn2D;msn2D_kcl -Msn4D_KCl_rep1;kcl;msn4D;msn4D_kcl -Msn4D_KCl_rep2;kcl;msn4D;msn4D_kcl -Msn2D_control_rep1;control;msn2D;msn2D_control -Msn2D_control_rep1;control;msn2D;msn2D_control -Msn4D_control_rep1;control;msn4D;msn4D_control -Msn4D_control_rep2;control;msn4D;msn4D_control -WT_control_rep1;control;wt;wt_control -WT_control_rep2;control;wt;wt_control -WT_KCl_rep1;kcl;wt;wt_kcl -WT_KCl_rep2;kcl;wt;wt_kcl +sample;env;genotype +WT_control_rep1;control;wt +WT_control_rep2;control;wt +WT_KCl_rep1;kcl;wt +WT_KCl_rep2;kcl;wt +Msn4D_control_rep1;control;msn4D +Msn4D_control_rep2;control;msn4D +Msn4D_KCl_rep1;kcl;msn4D +Msn4D_KCl_rep2;kcl;msn4D +Msn2D_control_rep1;control;msn2D +Msn2D_control_rep2;control;msn2D +Msn2D_KCl_rep1;kcl;msn2D +Msn2D_KCl_rep2;kcl;msn2D