LncPath (version 1.1)

geneSetDetail: Gain insight into the detail of the genes in a certain pathway

Description

Gain insight into the detail of the genes in a certain pathway, inculding the ranks, weights and cummulative running scores of each gene.

Usage

geneSetDetail(Result, Name)

Arguments

Result

A lncPath object come from the lncPath function.

Name

A string, the name of the pathway to be print.

Value

A data frame, the rows are gene names and the columns are detail of genes including gene name, rank, weight, cumulative ES score and core erichment.

Details

List all the genes of pathways ranked by the weights. The table also contains the gene name, the rank of genes in the whole gene list, the cumulative ES score and whether the gene is in the core gene sets which contribute to the score of the pathway.

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. et al. (2005) Gene set enrichment analysis: a knowledgebased approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A, 102, 15545-15550.

Examples

# NOT RUN {
##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

Result <- getExampleData("Result")
Detail <- geneSetDetail(Result, "KEGG_RIBOSOME")
head(Detail)

# }