fdr: False discovery rate computation for GSEA.

Description Usage Arguments Value Author(s) References Examples

View source: R/fdr.R

Description

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.

Usage

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fdr(NES, NESobs, NESnull)

Arguments

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.

Value

q

FDR q-value for the given gene set.

Author(s)

Guro Dorum

References

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.

Examples

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##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--    or do  help(data=index)  for the standard data sets.

GSEArot documentation built on May 2, 2019, 4:56 p.m.