Description Usage Arguments Value Author(s) References Examples
Computes a false discovery rate (FDR) q-value for a gene set given the observed normalised enrichment scores and a normalised null distribution. Calculations are done separately for positive and negative normalised enrichment scores.
1 | fdr(NES, NESobs, NESnull)
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NES |
Normalised enrichment score for the given gene set. |
NESobs |
Vector of normalised enrichment scores for all gene sets to be tested. |
NESnull |
Matrix of normalised null distribution for all gene sets to be tested. Each column represent a gene set, and each row represent a permutation. |
q |
FDR q-value for the given gene set. |
Guro Dorum
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S. and Mesirov, J. P (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression pro?les, PNAS, 102, 15545-15550.
1 2 3 | ##---- Should be DIRECTLY executable !! ----
##-- ==> Define data, use random,
##-- or do help(data=index) for the standard data sets.
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