wrapup_for_iSEE: wrapup_for_iSEE

In baj12/idealImmunoTP: Interactive Differential Expression AnaLysis

wrapup_for_iSEE

Description

Combine data from a typical DESeq2 run

Usage

wrapup_for_iSEE(dds, res)

Arguments

dds	A DESeqDataSet object.
res	A DESeqResults object.

Details

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 as specified in one of the workflows which include this package, e.g. in the context of the ideal package.

Value

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

Examples

# with simulated data...
library(DESeq2)
dds <- DESeq2::makeExampleDESeqDataSet(n=10000, m=8)
dds <- DESeq(dds)
res <- results(dds)
se <- wrapup_for_iSEE(dds, res)
# library(iSEE)
# iSEE(se)

## Not run: 
# or with the well known airway package...
library(airway)
data(airway)
airway
dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),
                                             colData = colData(airway),
                                             design=~cell+dex)
dds_airway <- DESeq2::DESeq(dds_airway)
res_airway <- DESeq2::results(dds_airway)
se_airway <- wrapup_for_iSEE(dds_airway, res_airway)
# iSEE(se_airway)

## End(Not run)

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