Mercurial > repos > eschen42 > mqppep_anova
changeset 29:42b207aaa527 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 83864e12abbf63728a389b7fe677f3b88844e03f
author | eschen42 |
---|---|
date | Thu, 27 Oct 2022 22:11:38 +0000 |
parents | 896eb8ae1c8c |
children | 8ff2c287ff1c |
files | mqppep_anova_script.Rmd |
diffstat | 1 files changed, 1 insertions(+), 165 deletions(-) [+] |
line wrap: on
line diff
--- a/mqppep_anova_script.Rmd Thu Oct 27 19:48:51 2022 +0000 +++ b/mqppep_anova_script.Rmd Thu Oct 27 22:11:38 2022 +0000 @@ -106,171 +106,7 @@ # to the directory where they should be writtn debugFileBasePath: !r if (TRUE) NULL else "test-data" --- -<!-- - alphaFile: "test-data/alpha_levels.tabular" - inputFile: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular" - preprocDb: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite" - kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2] - regexSampleNames: "\\.\\w+\\.\\d+[A-Z]$" - regexSampleGrouping: "\\w+" - groupFilterPatterns: ".+" - groupFilter: !r c("none", "exclude", "include")[3] - imputationMethod: !r c("group-median", "median", "mean", "random")[1] - kseaCutoffThreshold: !r c(0.05, 0.1, 0.20, 0.35, 0.4, 0.5, 0.999)[1] - ut_alphaFile: "test-data/alpha_levels.tabular" - ut_inputFile: "test-data/UT_phospho_ST_sites.preproc.tabular" - ut_preprocDb: "test-data/UT_phospho_ST_sites.preproc.sqlite" - ut_kseaAppPrepDb: !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2] - ut_regexSampleNames: "\\.\\d+[A-Z]$" - ut_regexSampleGrouping: "\\d+" - ut_groupFilterPatterns: ".+,.*" - ut_groupFilter: !r c("none", "exclude", "include")[1] - ut_imputationMethod: !r c("group-median", "median", "mean", "random")[4] - ut_kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5, 0.9)[1] - tst_alphaFile: "test-data/alpha_levels.tabular" - tst_inputFile: "test-data/test_input_for_anova.tabular" - tst_preprocDb: "test-data/test_input_for_anova.sqlite" - tst_kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2] - tst_regexSampleNames: "\\.\\d+[A-Z]$" - tst_regexSampleGrouping: "\\d+" - tst_groupFilterPatterns: ".+" - tst_groupFilter: !r c("none", "exclude", "include")[1] - tst_imputationMethod: !r c("group-median", "median", "mean", "random")[4] - tst_kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5, 0.9)[5] - - tst_alphaFile: "test-data/alpha_levels.tabular" - tst_inputFile: "test-data/UT_phospho_ST_sites.preproc.tabular" - tst_preprocDb: "test-data/UT_phospho_ST_sites.preproc.sqlite" - tst_kseaAppPrepDb: !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2] - tst_regexSampleNames: "\\.\\d+[A-Z]$" - tst_regexSampleGrouping: "\\d+" - tst_groupFilterPatterns: ".+,.*" - tst_groupFilter: !r c("none", "exclude", "include")[1] - tst_imputationMethod: !r c("group-median", "median", "mean", "random")[4] - tst_kseaCutoffThreshold: !r c(0.05, 0.1, 0.20, 0.35, 0.4, 0.5, 0.999)[5] - px_alphaFile: "test-data/alpha_levels.tabular" - px_inputFile: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular" - px_preprocDb: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite" - px_kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2] - px_regexSampleNames: "\\.\\w+\\.\\d+[A-Z]$" - px_regexSampleGrouping: "\\w+" - px_groupFilterPatterns: ".+" - px_groupFilter: !r c("none", "exclude", "include")[3] - px_imputationMethod: !r c("group-median", "median", "mean", "random")[4] - px_kseaCutoffThreshold: !r c(0.05, 0.1, 0.20, 0.35, 0.4, 0.5, 0.999)[5] - pdx_alphaFile: "test-data/alpha_levels.tabular" - pdx_inputFile: "test-data/PDX012970_pST.preproc_tab.tabular" - pdx_preprocDb: "test-data/PDX012970_pST.preproc.sqlite" - pdx_kseaAppPrepDb: !r c(":memory:", "test-data/PDX012970.sqlite")[2] - pdx_regexSampleNames: "\\.\\w+\\.\\w+\\.\\d+[A-Z]$" - pdx_regexSampleGrouping: "\\.\\w+\\K\\.\\w+" - pdx_groupFilterPatterns: "AdCa,AVPC" - pdx_groupFilter: !r c("none", "exclude", "include")[3] - pdx_imputationMethod: !r c("group-median", "median", "mean", "random")[4] - pdx_kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5, 0.9)[1] - tst_alphaFile: "test-data/alpha_levels.tabular" - tst_inputFile: "test-data/test_input_for_anova.tabular" - tst_preprocDb: "test-data/test_input_for_anova.sqlite" - tst_kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2] - tst_regexSampleNames: "\\.\\d+[A-Z]$" - tst_regexSampleGrouping: "\\d+" - tst_groupFilterPatterns: ".+" - tst_groupFilter: !r c("none", "exclude", "include")[1] - tst_kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5, 0.9)[5] - tst_imputationMethod: !r c("group-median", "median", "mean", "random")[1] - ut_alphaFile: "test-data/alpha_levels.tabular" - ut_inputFile: "test-data/UT_phospho_ST_sites.preproc.tabular" - ut_preprocDb: "test-data/UT_phospho_ST_sites.preproc.sqlite" - ut_kseaAppPrepDb: !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2] - ut_regexSampleNames: "\\.\\d+[A-Z]$" - ut_regexSampleGrouping: "\\d+" - ut_groupFilterPatterns: ".+,.*" - ut_groupFilter: !r c("none", "exclude", "include")[1] - ut_imputationMethod: !r c("group-median", "median", "mean", "random")[4] - alphaFile: "test-data/alpha_levels.tabular" - inputFile: "test-data/test_input_for_anova.tabular" - preprocDb: "test-data/test_input_for_anova.sqlite" - kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2] - regexSampleNames: "\\.\\d+[A-Z]$" - regexSampleGrouping: "\\d+" - groupFilterPatterns: ".+,.*" - groupFilter: !r c("none", "exclude", "include")[1] - imputationMethod: !r c("group-median", "median", "mean", "random")[4] - nd_alphaFile: "test-data/alpha_levels.tabular" - nd_inputFile: "test-data/pST_Sites_NancyDu.txt.preproc.tabular" - nd_preprocDb: "test-data/pST_Sites_NancyDu.txt.preproc.sqlite" - nd_kseaAppPrepDb: !r c(":memory:", "test-data/pST_Sites_NancyDu.ksea.sqlite")[2] - nd_regexSampleNames: "\\.\\d+[A-Z]$" - nd_regexSampleGrouping: "\\d+" - nd_groupFilterPatterns: ".+,.*" - nd_groupFilter: !r c("none", "exclude", "include")[1] - nd_imputationMethod: !r c("group-median", "median", "mean", "random")[4] - pxd_alphaFile: "test-data/alpha_levels.tabular" - pxd_inputFile: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular" - pxd_preprocDb: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite" - pxd_kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2] - pxd_regexSampleNames: "\\.\\w+\\.\\d+[A-Z]$" - pxd_regexSampleGrouping: "\\w+" - pxd_groupFilterPatterns: ".+" - pxd_groupFilter: !r c("none", "exclude", "include")[3] - pxd_imputationMethod: !r c("group-median", "median", "mean", "random")[4] - - alphaFile: "test-data/alpha_levels.tabular" - inputFile: "test-data/test_input_for_anova.tabular" - preprocDb: "test-data/test_input_for_anova.sqlite" - kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2] - regexSampleNames: "\\.\\d+[A-Z]$" - regexSampleGrouping: "\\d+" - groupFilterPatterns: ".+,.*" - groupFilter: !r c("none", "exclude", "include")[1] - - alphaFile: "test-data/alpha_levels.tabular" - inputFile: "test-data/PDX012970_pST.preproc_tab.tabular" - preprocDb: "test-data/PDX012970_pST.preproc.sqlite" - kseaAppPrepDb: !r c(":memory:", "test-data/PDX012970.sqlite")[2] - regexSampleNames: "\\.\\w+\\.\\w+\\.\\d+[A-Z]$" - regexSampleGrouping: "\\.\\w+\\K\\.\\w+" - groupFilterPatterns: "AdCa,AVPC" - groupFilter: !r c("none", "exclude", "include")[3] - - alphaFile: "test-data/alpha_levels.tabular" - inputFile: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular" - preprocDb: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite" - kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2] - regexSampleNames: "\\.\\w+\\.\\d+[A-Z]$" - regexSampleGrouping: "\\w+" - groupFilterPatterns: ".+,.*" - groupFilter: !r c("none", "exclude", "include")[3] - - kseaCutoffStatistic: !r c("p.value", "FDR")[2] - kseaCutoffThreshold: !r c(0.05, 0.1)[1] - - alphaFile: "test-data/alpha_levels.tabular" - inputFile: "test-data/UT_phospho_ST_sites.preproc.tabular" - preprocDb: "test-data/UT_phospho_ST_sites.preproc.sqlite" - kseaAppPrepDb: !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2] - regexSampleNames: "\\.\\d+[A-Z]$" - regexSampleGrouping: "\\d+" - - alphaFile: "test-data/alpha_levels.tabular" - inputFile: "test-data/pY_Sites_NancyDu.txt.ppep_intensities.ppep_map.preproc.tabular" - preprocDb: "test-data/pY_Sites_NancyDu.txt.ppep_intensities.ppep_map.preproc.sqlite" - kseaAppPrepDb: !r c(":memory:", "test-data/pY_Sites_NancyDu.ksea.sqlite")[2] - regexSampleNames: "\\.\\d+[A-Z]$" - regexSampleGrouping: "\\d+" - groupFilterPatterns: ".+,.*" - groupFilter: !r c("none", "exclude", "include")[3] - - alphaFile: "test-data/alpha_levels.tabular" - inputFile: "test-data/pST_Sites_NancyDu.txt.preproc.tabular" - preprocDb: "test-data/pST_Sites_NancyDu.txt.preproc.sqlite" - kseaAppPrepDb: !r c(":memory:", "test-data/pST_Sites_NancyDu.ksea.sqlite")[2] - regexSampleNames: "\\.\\d+[A-Z]$" - regexSampleGrouping: "\\d+" - groupFilterPatterns: ".+,.*" - groupFilter: !r c("none", "exclude", "include")[1] - ---> + ```{r setup, include = FALSE, results = 'asis'} # simple debug messaging