export_for_iSEE {GeneTonic} | R Documentation |
Combine data from a typical DESeq2 run
export_for_iSEE(dds, res_de, gtl = NULL)
dds |
A |
res_de |
A |
gtl |
A |
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 and/or after exploring
the functional enrichment results with GeneTonic()
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 - mainly the
results for differential expression analysis.
library("macrophage") library("DESeq2") # dds object data("gse", package = "macrophage") dds_macrophage <- DESeqDataSet(gse, design = ~ line + condition) rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15) dds_macrophage <- estimateSizeFactors(dds_macrophage) # res object data(res_de_macrophage, package = "GeneTonic") res_de <- res_macrophage_IFNg_vs_naive # now everything is in place to launch the app # dds_macrophage <- DESeq2::DESeq(dds_macrophage) se_macrophage <- export_for_iSEE(dds_macrophage, res_de) # iSEE(se_macrophage)