Description Usage Arguments Value Examples
Statistical validated networks
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states_vs_t |
a matrix with time in lines and individual states in columns |
alpha |
the family-wise error rate in the case of Bonferroni multiple-hypothesis correction, or the false discovery rate in the case of the FDR multiple hypothesis correction |
MHT.correction |
the type of multiple hypothesis correction |
exclude.states |
a vector of states to remove from states_vs_t |
states.pair.types |
accepted value: "all", "same", "different": selects which kind of state pairs are tested: if there are two states e.g. (1,2), "all" allows (1,1), (2,2) and (1,2); "same" allows (1,1) and (2,2), while "different" allows (1,2) |
alternative |
a string either equal to "overexpression" or "underexpression" |
a data.table object of the node pairs significantly correlated at the alpha level. The columns are: link_id: a unique identifier for links; i and j are the node names; si and sj are their states; pv is the value associated to the link; threshold is the Multiple Hypothesis Testing-adjusted p-value threshold (only links with pv<=threshold are kept)
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