Description Usage Arguments Value Author(s) See Also Examples
Gene graph enrichment analysis (GGEA) is a network-based enrichment analysis method implemented in the EnrichmentBrowser package. The idea of GGEA is to evaluate the consistency of known regulatory interactions with the observed gene expression data. A GGEA graph for a gene set of interest displays the consistency of each interaction in the network that involves a gene set member. Nodes (genes) are colored according to expression (up-/down-regulated) and edges (interactions) are colored according to consistency, i.e. how well the interaction type (activation/inhibition) is reflected in the correlation of the expression of both interaction partners.
1 2 3 4 5 6 7 8 9 10 11 12 | ggeaGraph(
gs,
grn,
se,
alpha = 0.05,
beta = 1,
max.edges = 50,
cons.thresh = 0.7,
show.scores = FALSE
)
ggeaGraphLegend()
|
gs |
Gene set under investigation. This should be a character vector of gene IDs. |
grn |
Gene regulatory network. Character matrix with exactly *THREE* cols; 1st col = IDs of regulating genes; 2nd col = corresponding regulated genes; 3rd col = regulation effect; Use '+' and '-' for activation/inhibition. |
se |
Expression data given as an object of class
|
alpha |
Statistical significance level. Defaults to 0.05. |
beta |
Log2 fold change significance level. Defaults to 1 (2-fold). |
max.edges |
Maximum number of edges that should be displayed. Defaults to 50. |
cons.thresh |
Consistency threshold. Graphical parameter that correspondingly increases line width of edges with a consistency above the chosen threshold (defaults to 0.7). |
show.scores |
Logical. Should consistency scores of the edges be displayed? Defaults to FALSE. |
None, plots to a graphics device.
Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>
nbea
to perform network-based enrichment analysis.
eaBrowse
for exploration of resulting gene sets.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | # (1) expression data:
# simulated expression values of 100 genes
# in two sample groups of 6 samples each
se <- makeExampleData(what="SE")
se <- deAna(se)
# (2) gene sets:
# draw 10 gene sets with 15-25 genes
gs <- makeExampleData(what="gs", gnames=names(se))
# (3) compiling artificial regulatory network
grn <- makeExampleData(what="grn", nodes=names(se))
# (4) plot consistency graph
ggeaGraph(gs=gs[[1]], grn=grn, se=se)
# (5) get legend
ggeaGraphLegend()
|
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