ideal makes differential expression analysis interactive, easy and reproducible. This function launches the main application included in the package.

ideal(
  dds_obj = NULL,
  res_obj = NULL,
  annotation_obj = NULL,
  countmatrix = NULL,
  expdesign = NULL,
  gene_signatures = NULL
)

Arguments

dds_obj

A DESeqDataSet object. If not provided, then a countmatrix and a expdesign need to be provided. If none of the above is provided, it is possible to upload the data during the execution of the Shiny App

res_obj

A DESeqResults object. If not provided, it can be computed during the execution of the application

annotation_obj

A data.frame object, with row.names as gene identifiers (e.g. ENSEMBL ids) and a column, gene_name, containing e.g. HGNC-based gene symbols. If not provided, it can be constructed during the execution via the org.eg.XX.db packages - these need to be installed

countmatrix

A count matrix, with genes as rows and samples as columns. If not provided, it is possible to upload the data during the execution of the Shiny App

expdesign

A data.frame containing the info on the covariates of each sample. If not provided, it is possible to upload the data during the execution of the Shiny App

gene_signatures

A list of vectors, one for each pathway/signature. This is for example the output of the read_gmt function. The provided object can also be replaced during runtime in the dedicated upload widget.

Value

A Shiny App is launched for interactive data exploration and differential expression analysis

Examples

# with simulated data... library(DESeq2) dds <- DESeq2::makeExampleDESeqDataSet(n = 100, m = 8) cm <- counts(dds) cd <- colData(dds) # with the well known airway package... library(airway) data(airway) airway
#> class: RangedSummarizedExperiment #> dim: 64102 8 #> metadata(1): '' #> assays(1): counts #> rownames(64102): ENSG00000000003 ENSG00000000005 ... LRG_98 LRG_99 #> rowData names(0): #> colnames(8): SRR1039508 SRR1039509 ... SRR1039520 SRR1039521 #> colData names(9): SampleName cell ... Sample BioSample
dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway), colData = colData(airway), design = ~ cell + dex ) if (FALSE) { ideal() ideal(dds) ideal(dds_airway) dds_airway <- DESeq2::DESeq(dds_airway) res_airway <- DESeq2::results(dds_airway) ideal(dds_airway, res_airway) }