gseaScore: Extract scores from GSEA results

In bedapub/ribiosGSEA: Gene-Set Enrichment Analysis Tools in Ribios

Extract scores from GSEA results

Description

One way to score GSEA results is to multiple the absolute value of log10 transformed p-values (nominal p-value, FDR, or FWER) with the sign of the enrichment scores. This score is intuitive since it combines statistical significance and the sign of regulation.

Usage

gseaScore(x, type = c("fdr", "p", "fwer"))

gseaScores(..., names = NULL, type = c("fdr", "p", "fwer"))

Arguments

x	An AnnoBroadGseaRes object
type	Character string, the type of p-value used to calculate the score.
...	Objects of AnnoBroadGseaRes to be compared
names	Character strings, names given to the result score sets. See examples below.

Details

gseaScores takes care of the situation where some gene sets are missing in one or more conditions.

Value

gseaScore returns a double vector of scores with gene set names.

gseaScores returns a data frame of scores, with gene set names as row names.

Functions

• gseaScores(): gseaScore applied to multiple objects

Author(s)

Jitao David Zhang <[e-mail]>

See Also

gseaNP, gseaFDR, gseaFWER to get p-values.

parseGSEAdir.

bedapub/ribiosGSEA documentation built on March 30, 2023, 3:26 p.m.