View source: R/lilikoi.PDSfun.r
lilikoi.PDSfun | R Documentation |
This function allows you to compute Pathway Desregulation Score deriving make sure that you have the below database for the metabolites and pathway list: meta_path.RData
lilikoi.PDSfun(qvec)
qvec |
This is the Metabolite_pathway_table from MetaTOpathway function. This table includes the metabolites ids and the its corssponding hmdb ids |
A large matrix of the pathway deregulation scores for each pathway in different samples.
Nygård, S., Lingjærde, O.C., Caldas, C. et al. PathTracer: High-sensitivity detection of differential pathway activity in tumours. Sci Rep 9, 16332 (2019). https://doi.org/10.1038/s41598-019-52529-3
dt <- lilikoi.Loaddata(file=system.file("extdata", "plasma_breast_cancer.csv", package = "lilikoi")) Metadata <- dt$Metadata dataSet <- dt$dataSet convertResults=lilikoi.MetaTOpathway('name') Metabolite_pathway_table = convertResults$table # PDSmatrix= lilikoi.PDSfun(Metabolite_pathway_table)
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