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

Description

Create a summary of multiple tmod analyses

Usage

1

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

Arguments

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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13

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)