nhejazi
R/eif_moderated.R
changed.
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R/plots.R
has changed.
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@@ -17,7 +17,7 @@
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| 17 | 17 | #' @param ... Other arguments passed to \code{\link[limma]{topTable}}. |
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| 18 | 18 | #' |
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| 19 | 19 | #' @importFrom methods is |
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| 20 | - | #' @importFrom dplyr "%>%" |
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| 20 | + | #' @importFrom dplyr "%>%" mutate select |
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| 21 | 21 | #' @importFrom stats plogis p.adjust |
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| 22 | 22 | #' @importFrom limma lmFit eBayes topTable |
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| 23 | 23 | #' @importFrom tibble as_tibble rownames_to_column |
@@ -78,14 +78,15 @@
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| 78 | 78 | sort.by = "none", |
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| 79 | 79 | ... |
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| 80 | 80 | ) %>% |
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| 81 | - | tibble::rownames_to_column(var = "ID") %>% |
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| 82 | - | tibble::as_tibble() %>% |
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| 83 | - | mutate( |
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| 81 | + | tibble::as_tibble(.name_repair = "minimal") %>% |
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| 82 | + | dplyr::mutate( |
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| 84 | 83 | # remove log-fold change and overwrite average expression with ATE |
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| 84 | + | ID = biotmle@NAMES, |
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| 85 | 85 | logFC = NULL, |
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| 86 | 86 | AveExpr = biotmle@ateOut, |
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| 87 | 87 | var_bayes = fit$s2.post / n_obs, |
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| 88 | - | ) |
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| 88 | + | ) %>% |
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| 89 | + | dplyr::select(ID, AveExpr, t, P.Value, adj.P.Val, B, var_bayes) |
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| 89 | 90 | ||
| 90 | 91 | # use logistic distribution as reference for p-values by default |
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| 91 | 92 | if (pval_type == "logistic") { |
| Files | Coverage |
|---|---|
| R | 78.57% |
| Project Totals (4 files) | 78.57% |
1342944671
| 1 |
comment: false |
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