tmodSummary: Create a summary of multiple tmod analyses
In tmod: Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

Description Usage Arguments Details Value See Also Examples

View source: R/panelplots.R

Create a summary of multiple tmod analyses

1	tmodSummary(x, clust = NULL, filter.empty = FALSE, filter.unknown = TRUE)

`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 NULL, the modules are sorted alphabetically by their ID.
`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

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.

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.

tmodPanelPlot

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)