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A function to wrap up the DESeq2 inputs&outputs, and plug that as SingleCellExperiment into iSEE
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| # one needs this as well | |
| library(SingleCellExperiment) | |
| wrapup_for_iSEE <- function(dds, res) { | |
| # dds to vst | |
| vst <- vst(dds) | |
| sce <- SingleCellExperiment( | |
| assays = List( | |
| counts = counts(dds), | |
| normcounts = counts(dds,normalized = TRUE), | |
| vst_counts = assay(vst) | |
| ) | |
| ) | |
| # adding colData | |
| colData(sce) <- colData(dds) | |
| # adding rowData | |
| rowData(sce) <- res | |
| # log operations to have the rowData ready to use | |
| rowData(sce)$log10_baseMean <- log10(rowData(sce)$baseMean) | |
| rowData(sce)$log10_pvalue <- -log10(rowData(sce)$pvalue) | |
| return(sce) | |
| } |
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