DEsubs: Default run of DEsubs

In DEsubs: DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments

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', 'DESeq', 'EBSeq', 'NBPSeq', 'voom+limma', 'vst+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)

DEsubs documentation built on Nov. 8, 2020, 8:31 p.m.