View source: R/test_activation.R
get_active_signatures | R Documentation |
Returns signatures that are most differentially active in the limma result. We provide three methods to define "most" active: sort by the difference in activities (method = "diff"), filter by a significance level (method = "pvalue"), and consider both difference and significance using pareto fronts (method = "pareto"). This function should be used after build_limma() function.
get_active_signatures(limma_result, method = "pareto", pheno_group = "both", N_fronts = 5, N_signatures = 10, significance_cutoff = 0.05)
limma_result |
a data.frame that stores the limma result table returned by the build_limma() function. It should have rownames that specifies the name of each feature. |
method |
character, can be "diff", "pvalue", or "pareto" (default: "pareto") |
pheno_group |
character, can be "both", "level1", or "level2". If "both", signatures active in both phenotypes will be merged, sorted, and considered together. If "level1", only signatures active in the first phenotypes level (signatures with negative logFC) will be returned. Similarly, "level2" will return only signatures active in the second phenotypes level (signatures with positive logFC). (default: "both") |
N_fronts |
int, number of pareto fronts to return in the "pareto" method (default: 5) |
N_signatures |
int, number of top signatures to return in the "diff" method (default: 10) |
significance_cutoff |
numeric, significance cutoff to use in the "pvalue" method (default: 0.05). |
a vector storing active signatures.
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