DEsubs {DEsubs} | R Documentation |
Default run of DEsubs
DEsubs(org, mRNAexpr, mRNAnomenclature, pathways, DEtool, DEpar, CORtool, CORpar, subpathwayType, rankedList, verbose)
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. |
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.
A list used as input in
geneVisualization
, subpathwayVisualization
,
subpathwayToGraph
, organismVisualization
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)