Compute Single Sample Perturbation Score — compute_perturbation

Propagate weighted single sample logFCs down the pathway topologies to compute single sample perturbation scores for each pathway

compute_perturbation_score(weightedFC, gsTopology)

Arguments

weightedFC: A matrix of weighted single sample logFCs derived from function weight_ss_fc()
gsTopology: List of pathway topology matrices generated using function retrieve_topology()

Value

A list where each element is a matrix corresponding to a pathway. Each column of an element corresponds to a sample.

Details

This function use the algorithm adopted from SPIA (see citation) to compute a single sample perturbation score per sample per pathway. The rownames of the weighted single sample logFC matrix and the pathway topology matrices must use the same type of gene identifier (ie. entrez ID).

References

Tarca AL, Draghici S, Khatri P, Hassan SS, Mittal P, Kim JS, Kim CJ, Kusanovic JP, Romero R. A novel signaling pathway impact analysis. Bioinformatics. 2009 Jan 1;25(1):75-82.

Examples

#compute weighted single sample logFCs
ls <- weight_ss_fc(logCPM_example, metadata = metadata_example,
factor = "patient", control = "Vehicle")

# explore all species and databases supported by graphite
if (FALSE) {
graphite::pathwayDatabases()
retrieve_topology(species = "hsapiens", database = "kegg",
outputDir = "gsTopology.rda")
}
load(system.file("extdata", "gsTopology.rda", package = "sSNAPPY"))
ssPertScore <- compute_perturbation_score(ls$logFC, gsTopology)