Description Usage Arguments Value
This function generates a GSEA null distribution of enrichment scores based on gene shuffling, i.e. the positions of genes in the signature are permuted rather than phenotype labels. It will add a normalized enrichment score (NES) to the gsea object as described by Subramanian et al. and statistical inference is carried out using one-tailed tests on the appropriate (positive/negative) side of the null distribution. For two-tailed GSEA, the null model is calculated accordingly and separate NES and p-values are provided for each gene set.
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gsea_obj |
a gsea object as returned by gsea1T or gsea2T/gsea_regulon |
... |
Additional parameters added to keep compatibility |
w |
numeric indicating the weights used for GSEA (defaults to 1) |
perm |
integer indicating the number of permutations to carry out (defaults to 1000) |
seed |
integer for random number generation during the permutation process (defaults to 42) |
analytical |
logical whether to derive p-values analytically, i.e. from two-tailed test using a normal distribution (defaults to FALSE, i.e. inference according to Subramanian et al.) |
gsea_obj with information on nullmodel added in extra slots
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