Description Usage Arguments Value Author(s) See Also Examples
View source: R/network.graphite.R
Create a graphNEL graph with directed edges from the results for a specified reaction
1 2 | network.graphite(pSymbol, expr.matrix, toptableNodes, typeID, threshold,
selectedReaction, toptable3, selectedComparison, expr.toBind, pvalue)
|
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 |
A graphNEL graph with directed edges
Simon J Pelletier
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | 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)
|
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