idealImmunoTP: idealImmunoTP: Interactive Differential Expression Analysis

In baj12/idealImmunoTP: Interactive Differential Expression AnaLysis

idealImmunoTP: Interactive Differential Expression Analysis

Description

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

Usage

idealImmunoTP(
  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
dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),
                                             colData = colData(airway),
                                             design=~cell+dex)
## Not run: 

idealImmunoTP()
idealImmunoTP(dds)
idealImmunoTP(dds_airway)

dds_airway <- DESeq2::DESeq(dds_airway)
res_airway <- DESeq2::results(dds_airway)
idealImmunoTP(dds_airway, res_airway)

## End(Not run)

baj12/idealImmunoTP documentation built on Dec. 5, 2023, 12:33 a.m.