network.graphite: Create a graphNEL graph with directed edges from the results...

In spell098/rnaseq_app:

Description

Create a graphNEL graph with directed edges from the results for a specified reaction

Usage

network.graphite(pSymbol, expr.matrix, toptableNodes, typeID, threshold,
  selectedReaction, toptable3, selectedComparison, expr.toBind, pvalue)

Arguments

pSymbol	Symbol IDs
expr.matrix	Expression set containing all the information on a dataset
toptableNodes	topTable with added column of the reaction nodes it belongs to
typeID	Type of IDs used as rows in the expression matrix.Default="ensembl_gene_id"
threshold	Threshold of coexpression
selectedReaction	Selected reaction from the topReactions
selectedComparison	Comparison studied. Name of the matrices (topTables) in the list "results"
expr.toBind	Expression data.matrix with supplemental colums: module and ID
pvalue	p-value limit
topTable3	topTable results for every gene

Value

A graphNEL graph with directed edges

Author(s)

Simon J Pelletier

See Also

export2cytoscape graphite

Examples

expr.matrix <- readRDS("data/expr_matrix_LGVD.rds")
topReactions <- readRDS("data/reactions_mfuzz.rds")
topTable3 <- readRDS("data/topTable3_LGVD.rds")
selectedReaction <- "RHO GTPases activate PAKs"
ratReactome <- pathways("rnorvegicus", "reactome")
p <- ratReactome[[selectedReaction]]
pSymbol <- convertIdentifiers(p, "SYMBOL")
toptableNodes = cbind(
   topTable3[[1]][match(nodes(pSymbol),topTable3[[1]]$symbol),],
   Reaction = rep(selectedReaction[[1]],length(nodes(pSymbol)))
)
toptableNodes1 = toptableNodes[!is.na(toptableNodes[,1]),]
typeID = "ensembl_gene_id"
threshold = 0.8

network.graphite(pSymbol,expr.matrix,toptableNodes,typeID,threshold,selectedReaction,topTable3,1,expr.toBind,pvalue)

spell098/rnaseq_app documentation built on May 30, 2019, 7:57 a.m.