tmodSummary: Create a summary of multiple tmod analyses

In tmod: Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

Create a summary of multiple tmod analyses

Description

Create a summary of multiple tmod analyses

Usage

tmodSummary(
  x,
  clust = NULL,
  filter.empty = FALSE,
  filter.unknown = TRUE,
  select = NULL,
  effect.col = NULL,
  pval.col = "adj.P.Val"
)

Arguments

x	list, in which each element has been generated with a tmod test function
clust	whether, in the resulting data frame, the modules should be ordered by clustering them with either q-values ("qval") or the effect size ("effect"). If "sort" or NULL, the modules are sorted alphabetically by their ID. If "keep", then the order of the modules is kept.
filter.empty	If TRUE, all elements (columns) with no significant enrichment will be removed
filter.unknown	If TRUE, modules with no annotation will be omitted
select	a character vector of module IDs to show. If clust == "keep", then in that particular order.
effect.col	The name of the column with the effect size (if NULL, the default, the effect size will be taken from the tmod results object attributes)
pval.col	The name of the p-value column

Details

This function is useful if you run an analysis for several conditions or time points and would like to summarize the information in a single data frame. You can use lapply() to generate a list with tmod results and use tmodSummary to convert it to a data frame.

Value

a data frame with a line for each module encountered anywhere in the list x, two columns describing the module (ID and module title), and two columns(effect size and q value) for each element of list x.

See Also

tmodPanelPlot

Examples

## Not run: 
data(Egambia)
E <- Egambia[,-c(1:3)]
pca <- prcomp(t(E), scale.=TRUE)

# Calculate enrichment for each component
gs   <- Egambia$GENE_SYMBOL
gn.f <- function(r) {
    tmodCERNOtest(gs[order(abs(r), 
                decreasing=TRUE)], 
                qval=0.01)
}
x <- apply(pca$rotation, 2, gn.f)
tmodSummary(x)

## End(Not run)

tmod documentation built on March 31, 2023, 9 p.m.