Files in mariechion/mi4p

Multiple Imputation for Proteomics

Arabidopsis_UPS/Aggregation/Arabido_UPS_1of3inall_Aggreg_Script.R Arabidopsis_UPS/MBR_1of3inall/Arabido_UPS_1of3inall_impMLE_Script.R Arabidopsis_UPS/MBR_2of3inall/Arabido_UPS_2of3inall_impMLE_Script.R Arabidopsis_UPS/MBR_6vs7_1of3inall/Arabido_UPS_6vs7_1of3inall_impMLE_Script.R Arabidopsis_UPS/Script_gtest.R Arabidopsis_UPS/noMBR_1of3inall/Arabido_UPS_noMBR_1of3inall_impMLE_Script.R Arabidopsis_UPS/noMBR_2of3inall/Arabido_UPS_noMBR_2of3inall_impMLE_Script.R Functions/MVgen.R Functions/eBayes_mod.R Functions/hid_ebayes.R Functions/limmaCompleteTest_mod.R Functions/meanImp_emmeans.R Functions/mi4limma.R Functions/multi_impute.R Functions/proj_matrix.R Functions/rubin1_all.R Functions/rubin1_one.R Functions/rubin2_all.R Functions/rubin2bt_all.R Functions/rubin2bt_one.R Functions/rubin2wt_all.R Functions/rubin2wt_one.R Functions/within_variance_comp_emmeans.R NEWS.md R/MVgen.R R/check.conditions.R R/check.design.R R/datasets.R R/eBayes_mod.R R/formatLimmaResult.R R/hid_ebayes.R R/limmaCompleteTest_mod.R R/make.contrast.R R/make.design.R R/meanImp_emmeans.R R/mi4limma.R R/mi4p-package.R R/multi_impute.R R/proj_matrix.R R/protdatasim.R R/rubin1_all.R R/rubin1_one.R R/rubin2_all.R R/rubin2bt_all.R R/rubin2bt_one.R R/rubin2wt_all.R R/rubin2wt_one.R R/test.design.R R/within_variance_comp_emmeans.R README.Rmd README.md Simulation-1/DATA/data_generation.R Simulation-1/MV10pct/MV10pct_impKNN_Script.R Simulation-1/MV10pct/MV10pct_impMLE_Script.R Simulation-1/MV10pct/MV10pct_impNORM_Script.R Simulation-1/MV10pct/MV10pct_impPCA_Script.R Simulation-1/MV10pct/MV10pct_impRF_Script.R Simulation-1/MV15pct/MV15pct_impKNN_Script.R Simulation-1/MV15pct/MV15pct_impMLE_Script.R Simulation-1/MV15pct/MV15pct_impNORM_Script.R Simulation-1/MV15pct/MV15pct_impPCA_Script.R Simulation-1/MV15pct/MV15pct_impRF_Script.R Simulation-1/MV1pct/MV1pct_impKNN_Script.R Simulation-1/MV1pct/MV1pct_impMLE_Script.R Simulation-1/MV1pct/MV1pct_impNORM_Script.R Simulation-1/MV1pct/MV1pct_impPCA_Script.R Simulation-1/MV1pct/MV1pct_impRF_Script.R Simulation-1/MV20pct/MV20pct_impKNN_Script.R Simulation-1/MV20pct/MV20pct_impMLE_Script.R Simulation-1/MV20pct/MV20pct_impNORM_Script.R Simulation-1/MV20pct/MV20pct_impPCA_Script.R Simulation-1/MV20pct/MV20pct_impRF_Script.R Simulation-1/MV25pct/MV25pct_impKNN_Script.R Simulation-1/MV25pct/MV25pct_impMLE_Script.R Simulation-1/MV25pct/MV25pct_impNORM_Script.R Simulation-1/MV25pct/MV25pct_impPCA_Script.R Simulation-1/MV25pct/MV25pct_impRF_Script.R Simulation-1/MV5pct/MV5pct_impKNN_Script.R Simulation-1/MV5pct/MV5pct_impMLE_Script.R Simulation-1/MV5pct/MV5pct_impNORM_Script.R Simulation-1/MV5pct/MV5pct_impPCA_Script.R Simulation-1/MV5pct/MV5pct_impRF_Script.R Simulation-2/DATA/L16bis_amputed_data_generation.R Simulation-2/DATA/L16bis_complete_data_generation.R Simulation-2/MV10pct/L16bis_MV10pct_impMLE_Script.R Simulation-2/MV10pct/L16bis_MV10pct_impNORM_Script.R Simulation-2/MV10pct/L16bis_MV10pct_impPCA_Script.R Simulation-2/MV10pct/L16bis_MV10pct_impRF_Script.R Simulation-2/MV10pct/L16bis_MV10pct_impkNN_Script.R Simulation-2/MV15pct/L16bis_MV15pct_impMLE_Script.R Simulation-2/MV15pct/L16bis_MV15pct_impNORM_Script.R Simulation-2/MV15pct/L16bis_MV15pct_impPCA_Script.R Simulation-2/MV15pct/L16bis_MV15pct_impRF_Script.R Simulation-2/MV15pct/L16bis_MV15pct_impkNN_Script.R Simulation-2/MV1pct/L16bis_MV1pct_impKNN_Script.R Simulation-2/MV1pct/L16bis_MV1pct_impMLE_Script.R Simulation-2/MV1pct/L16bis_MV1pct_impNORM_Script.R Simulation-2/MV1pct/L16bis_MV1pct_impPCA_Script.R Simulation-2/MV1pct/L16bis_MV1pct_impRF_Script.R Simulation-2/MV20pct/L16bis_MV20pct_impMLE_Script.R Simulation-2/MV20pct/L16bis_MV20pct_impNORM_Script.R Simulation-2/MV20pct/L16bis_MV20pct_impPCA_Script.R Simulation-2/MV20pct/L16bis_MV20pct_impRF_Script.R Simulation-2/MV20pct/L16bis_MV20pct_impkNN_Script.R Simulation-2/MV25pct/L16bis_MV25pct_impMLE_Script.R Simulation-2/MV25pct/L16bis_MV25pct_impNORM_Script.R Simulation-2/MV25pct/L16bis_MV25pct_impPCA_Script.R Simulation-2/MV25pct/L16bis_MV25pct_impRF_Script.R Simulation-2/MV25pct/L16bis_MV25pct_impkNN_Script.R Simulation-2/MV5pct/L16bis_MV5pct_impMLE_Script.R Simulation-2/MV5pct/L16bis_MV5pct_impNORM_Script.R Simulation-2/MV5pct/L16bis_MV5pct_impPCA_Script.R Simulation-2/MV5pct/L16bis_MV5pct_impRF_Script.R Simulation-2/MV5pct/L16bis_MV5pct_impkNN_Script.R Simulation-3/DATA/L16_amputed_data_generation.R Simulation-3/DATA/L16_complete_data_generation.R Simulation-3/MV10pct/L16_MV10pct_impMLE_Script.R Simulation-3/MV10pct/L16_MV10pct_impNORM_Script.R Simulation-3/MV10pct/L16_MV10pct_impPCA_Script.R Simulation-3/MV10pct/L16_MV10pct_impRF_Script.R Simulation-3/MV10pct/L16_MV10pct_impkNN_Script.R Simulation-3/MV15pct/L16_MV15pct_impMLE_Script.R Simulation-3/MV15pct/L16_MV15pct_impNORM_Script.R Simulation-3/MV15pct/L16_MV15pct_impPCA_Script.R Simulation-3/MV15pct/L16_MV15pct_impRF_Script.R Simulation-3/MV15pct/L16_MV15pct_impkNN_Script.R Simulation-3/MV1pct/L16_MV1pct_impMLE_Script.R Simulation-3/MV1pct/L16_MV1pct_impNORM_Script.R Simulation-3/MV1pct/L16_MV1pct_impPCA_Script.R Simulation-3/MV1pct/L16_MV1pct_impRF_Script.R Simulation-3/MV1pct/L16_MV1pct_impkNN_Script.R Simulation-3/MV20pct/L16_MV20pct_impMLE_Script.R Simulation-3/MV20pct/L16_MV20pct_impNORM_Script.R Simulation-3/MV20pct/L16_MV20pct_impPCA_Script.R Simulation-3/MV20pct/L16_MV20pct_impRF_Script.R Simulation-3/MV20pct/L16_MV20pct_impkNN_Script.R Simulation-3/MV25pct/L16_MV25pct_impMLE_Script.R Simulation-3/MV25pct/L16_MV25pct_impNORM_Script.R Simulation-3/MV25pct/L16_MV25pct_impPCA_Script.R Simulation-3/MV25pct/L16_MV25pct_impRF_Script.R Simulation-3/MV25pct/L16_MV25pct_impkNN_Script.R Simulation-3/MV5pct/L16_MV5pct_impMLE_Script.R Simulation-3/MV5pct/L16_MV5pct_impNORM_Script.R Simulation-3/MV5pct/L16_MV5pct_impPCA_Script.R Simulation-3/MV5pct/L16_MV5pct_impRF_Script.R Simulation-3/MV5pct/L16_MV5pct_impkNN_Script.R Yeast_UPS/1of3inall/Yeast_UPS_TG_1of3inall_impMLE_Script.R Yeast_UPS/2of3inall/Yeast_UPS_TG_2of3inall_impMLE_Script.R Yeast_UPS/Aggregation/Yeast_UPS_TG_1of3inall_Aggreg_Script.R docs/reference/figures/Cairo-fa-images.pdf man/MVgen.Rd man/check.conditions.Rd man/check.design.Rd man/datasim.Rd man/eBayes.mod.Rd man/figures/Cairo-fa-images.pdf man/formatLimmaResult.Rd man/hid.ebayes.Rd man/limmaCompleteTest.mod.Rd man/make.contrast.Rd man/make.design.1.Rd man/make.design.2.Rd man/make.design.3.Rd man/make.design.Rd man/meanImp_emmeans.Rd man/mi4limma.Rd man/mi4p-package.Rd man/mm_peptides.Rd man/multi.impute.Rd man/norm.200.m100.sd1.vs.m200.sd1.list.Rd man/proj_matrix.Rd man/protdatasim.Rd man/qData.Rd man/rubin1.all.Rd man/rubin1.one.Rd man/rubin2.all.Rd man/rubin2bt.all.Rd man/rubin2bt.one.Rd man/rubin2wt.all.Rd man/rubin2wt.one.Rd man/sTab.Rd man/test.design.Rd man/within_variance_comp_emmeans.Rd vignettes/Intromi4p.R vignettes/Intromi4p.Rmd