gsea.rotation: GSEA with rotation test

In GSEArot: GSEA rotation

Description

GSEA with rotation test

Usage

gsea.rotation(X, y = NULL, S, nrot = 500, fun = t.90th)

Arguments

X	Gene expression matrix with samples as rows and genes as columns.
y	Optional vector of 0/1 indicating sample phenotype.
S	Matrix indicating gene set membership with genes as rows and gene sets as columns. 1 indicates that the gene is a member, 0 indicates not a member.
nrot	The number of rotations to perform. Default is 500.
fun	Name of function for computing a gene wise test statistic. Default is t-values with 90th percentile stabilised variance.

Value

p.values	A p-value for each gene set
q.values	A FDR q-value for each gene set

Author(s)

Guro D\orum

References

D\orum, G., Snipen, L., Solheim, M. and S\aeb\o (2009) Rotation Testing in Gene Set Enrichment Analysis for Small Direct Comparison Experiments. Statistical Applications in Genetics and Molecular Biology, 8(1), article 34.

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<af>les, PNAS, 102, 15545-15550.

Examples

##---- 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.