Propagate weighted single sample logFCs down the pathway topologies to compute single sample perturbation scores for each pathway
compute_perturbation_score(weightedFC, gsTopology)A matrix of weighted single sample logFCs derived from function weight_ss_fc()
List of pathway topology matrices generated using function retrieve_topology()
A list where each element is a matrix corresponding to a pathway. Each column of an element corresponds to a sample.
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).
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.
#compute weighted single sample logFCs
data(metadata_example)
data(logCPM_example)
ls <- weight_ss_fc(logCPM_example, metadata = metadata_example,
factor = "patient", control = "Vehicle")
# explore all databases supported by graphite
graphite::pathwayDatabases()
#> species database
#> 1 athaliana kegg
#> 2 athaliana pathbank
#> 3 athaliana wikipathways
#> 4 btaurus kegg
#> 5 btaurus pathbank
#> 6 btaurus reactome
#> 7 btaurus wikipathways
#> 8 celegans kegg
#> 9 celegans pathbank
#> 10 celegans reactome
#> 11 celegans wikipathways
#> 12 cfamiliaris kegg
#> 13 cfamiliaris reactome
#> 14 cfamiliaris wikipathways
#> 15 dmelanogaster kegg
#> 16 dmelanogaster pathbank
#> 17 dmelanogaster reactome
#> 18 dmelanogaster wikipathways
#> 19 drerio kegg
#> 20 drerio reactome
#> 21 drerio wikipathways
#> 22 ecoli kegg
#> 23 ecoli pathbank
#> 24 ecoli wikipathways
#> 25 ggallus kegg
#> 26 ggallus reactome
#> 27 ggallus wikipathways
#> 28 hsapiens kegg
#> 29 hsapiens panther
#> 30 hsapiens pathbank
#> 31 hsapiens pharmgkb
#> 32 hsapiens reactome
#> 33 hsapiens smpdb
#> 34 hsapiens wikipathways
#> 35 mmusculus kegg
#> 36 mmusculus pathbank
#> 37 mmusculus reactome
#> 38 mmusculus wikipathways
#> 39 rnorvegicus kegg
#> 40 rnorvegicus pathbank
#> 41 rnorvegicus reactome
#> 42 rnorvegicus wikipathways
#> 43 scerevisiae kegg
#> 44 scerevisiae pathbank
#> 45 scerevisiae reactome
#> 46 scerevisiae wikipathways
#> 47 sscrofa kegg
#> 48 sscrofa reactome
#> 49 sscrofa wikipathways
#> 50 xlaevis kegg
gsTopology <- retrieve_topology(database = "kegg")
ssPertScore <- compute_perturbation_score(ls$logFC, gsTopology)