Combine data from a typical DESeq2 run
Combines the DESeqDataSet input and DESeqResults into a SummarizedExperiment object, which can be readily explored with iSEE.
A typical usage would be after running the DESeq2 pipeline as specified in one of the workflows which include this package, e.g. in the context of the ideal package.
A SummarizedExperiment object, with raw counts, normalized counts, and variance-stabilizing transformed counts in the assay slots; and with colData and rowData extracted from the corresponding input parameters
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# with simulated data... library(DESeq2) dds <- DESeq2::makeExampleDESeqDataSet(n=10000, m=8) dds <- DESeq(dds) res <- results(dds) se <- wrapup_for_iSEE(dds, res) # library(iSEE) # iSEE(se) ## Not run: # or with the well known airway package... library(airway) data(airway) airway dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway), colData = colData(airway), design=~cell+dex) dds_airway <- DESeq2::DESeq(dds_airway) res_airway <- DESeq2::results(dds_airway) se_airway <- wrapup_for_iSEE(dds_airway, res_airway) # iSEE(se_airway) ## End(Not run)
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