Combine data from a typical DESeq2 run
export_for_iSEE(dds, res_de, gtl = NULL)A DESeqDataSet object.
A DESeqResults object.
A GeneTonic-list object, containing in its slots the arguments
specified above: dds, res_de, res_enrich, and annotation_obj - the names
of the list must be specified following the content they are expecting
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.
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()
library("macrophage")
library("DESeq2")
# dds object
data("gse", package = "macrophage")
dds_macrophage <- DESeqDataSet(gse, design = ~ line + condition)
#> using counts and average transcript lengths from tximeta
rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15)
dds_macrophage <- estimateSizeFactors(dds_macrophage)
#> using 'avgTxLength' from assays(dds), correcting for library size
# 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)
#> Attempting to combine a dds and a res_de object where not allidentifiers are shared. Subsetting to the intersection of these...
# iSEE(se_macrophage)