ideal: Interactive Differential Expression Analysis

Source: R/ideal.R

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 DESeq2::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 DESeq2::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", package = "airway")
airway
#> class: RangedSummarizedExperiment 
#> dim: 63677 8 
#> metadata(1): ''
#> assays(1): counts
#> rownames(63677): ENSG00000000003 ENSG00000000005 ... ENSG00000273492
#>   ENSG00000273493
#> rowData names(10): gene_id gene_name ... seq_coord_system symbol
#> 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) { # \dontrun{

ideal()
ideal(dds)
ideal(dds_airway)

dds_airway <- DESeq2::DESeq(dds_airway)
res_airway <- DESeq2::results(dds_airway)
ideal(dds_airway, res_airway)
} # }