DEsubs {DEsubs} | R Documentation

## Default run of DEsubs

### Description

Default run of DEsubs

### Usage

    DEsubs(org, mRNAexpr, mRNAnomenclature, pathways, DEtool, DEpar,
        CORtool, CORpar, subpathwayType, rankedList, verbose)

### Arguments

`org` | Organism identifier ('hsa', 'mmu', 'rno', 'sce', 'ath', 'dme', 'dre')
`mRNAexpr` | RNA-seq expression data in the form of either a matrix or a filename of a text file stored in the 'User' directory.
`mRNAnomenclature` | mRNAnomenclature ('entrezgene', 'ensembl_gene_id', 'ensembl_transcript_id', 'ensembl_peptide_id', 'hgnc_id', 'hgnc_symbol', 'hgnc_transcript_name', 'refseq_mrna', 'refseq_peptide')
`pathways` | Pathway type ('All', 'Non-Metabolic', 'Metabolic')
`DEtool` | DEG analysis tool selection for NodeRule ('edgeR', 'DESeq2', 'EBSeq', 'NBPSeq', 'voom+limma', 'vst2+limma', 'TSPM')
`DEpar` | DE analysis tools Q-value threshold of NodeRule (default: DEGpar = 0.05)
`CORtool` | Correlation measure selection for EdgeRule ('pearson', 'kendall', 'spearman')
`CORpar` | Correlation measure threshold of EdgeRule (default: CORpar = 0.6)
`subpathwayType` | Subpathway extraction type selection (get all availiable options from subpathwayTypes)
`rankedList` | A named vector of genes and their corresponding significance of differential expression in the form of a Q-value. If the argument is not null, no DEtool is used for differential expression analysis.
`verbose` | TRUE to display informative messages, FALSE to hide.

### Details

- Class vector needed values 1 and 2 for each class (eg. control and disease samples).

- DEpar should be less than 0.05 in order to return statistically significant DEGs.

- Higher CORpar values result in stricter correlation criteria, i.e. less acceptable interactions.

### Value

A list used as input in `geneVisualization`, `subpathwayVisualization`, `subpathwayToGraph`, `organismVisualization`

### Examples

    load(system.file('extdata', 'data.RData', package='DEsubs'))

    DEsubs.run <- DEsubs(   org='hsa',
                            mRNAexpr=mRNAexpr,
                            mRNAnomenclature='entrezgene',
                            pathways='All',
                            DEtool=NULL, DEpar=0.05,
                            CORtool='pearson', CORpar=0.6,
                            subpathwayType=NULL,
                            rankedList=rankedList)

[Package DEsubs version 1.20.0 Index]