cut_by_NES: Trim the table of results.

In massiveGST: Competitive Gene Sets Test with the Mann-Whitney-Wilcoxon Test

Trim the table of results.

Description

This function trims the table of results from massiveGST function retaining the rows with a NES below the specified threshold.

Usage

cut_by_NES(ttable, NES_threshold = 0.6)

Arguments

ttable	a data frame of 'mGST' class coming from massiveGST function.
NES_threshold	a real value between 0.0 and 1.

Value

A data frame.

Note

the functions cut_by_NES, cut_by_logit2NES, and cut_by_significance can be nested. In the case the test has alternative = 'two.sided', it is better to use cut_by_logit2NES for a symmetric trim of both directions.

Author(s)

Stefano M. Pagnotta

References

Cerulo, Pagnotta (2022) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.3390/e24050739")}

See Also

massiveGST, cut_by_logit2NES, cut_by_significance, summary.mGST, plot.mGST

Examples

library(massiveGST)

# get the gene profile
fname <- system.file("extdata", package="massiveGST")
fname <- file.path(fname, "pre_ranked_list.txt")
geneProfile <- get_geneProfile(fname)

# get the gene-sets
fname <- system.file("extdata", package="massiveGST")
fname <- file.path(fname, "h.all.v2024.1.Hs.symbols.gmt")
geneSets <- get_geneSets_from_local_files(fname)

# run the function
ans <- massiveGST(geneProfile, geneSets, alternative = "greater")

head(ans)
cut_by_NES(ans, NES_threshold = .65)
summary(cut_by_NES(ans, NES_threshold = .65))

massiveGST documentation built on April 3, 2025, 10:57 p.m.