formatPathways function

Format cytoscape nested networks

Format cytoscape nested networks using preset NetGSA format

formatPathways(x, pways, graph_layout = NULL)

Arguments

• x: A NetGSA object returned from calling NetGSA()
• pways: Character vector of pathways to format
• graph_layout: (Optional) Layout to pass to plots. Must be a string for Cytoscape which will be passed to RCy3::layoutNetwork.

Details

Loads gene testing data into each pathway. Genes are tested using an F-test if there are 2 or more conditions or a two-sided one-class t-test against the null hypothesis of mean = 0 if there is only one condition. FDR corrected q-values are mapped to the color of the node. The scale ranges from 0 to 1 with red represents q-values of 0 and white representing q-values of 1. Loaded data includes: p-value from the F-test/t-test (pval), FDR corrected q-value (pFdr), test statistic from the F-test/t-test (teststat).

Custom formatting can be applied using the cytoscape GUI or the RCy3 pacakge.

Returns

No return value, called for side effects

References

Ma, J., Shojaie, A. & Michailidis, G. (2016) Network-based pathway enrichment analysis with incomplete network information. Bioinformatics 32(20):165--3174.

Author(s)

Michael Hellstern

See Also

plot.NetGSA

Examples

## Not run:

## load the data
data("breastcancer2012_subset")

## consider genes from just 2 pathways
genenames    <- unique(c(pathways[["Adipocytokine signaling pathway"]], 
                         pathways[["Adrenergic signaling in cardiomyocytes"]]))
sx           <- x[match(rownames(x), genenames, nomatch = 0L) > 0L,]

db_edges       <- obtainEdgeList(rownames(sx), databases = c("kegg", "reactome"))
adj_cluster    <- prepareAdjMat(sx, group, databases = db_edges, cluster = TRUE)
out_cluster    <- NetGSA(adj_cluster[["Adj"]], sx, group, 
                         pathways_mat[c(1,2), rownames(sx)], lklMethod = "REHE", sampling = FALSE)
plot(out_cluster)
formatPathways(out_netgsa, "Adipocytokine signaling pathway")
## End(Not run)