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

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 1.18.0 Index]