# NOT RUN {
data(PhyloExpressionSetExample)
set.seed(123)
test_set <- sample(PhyloExpressionSetExample[ , 2],10000)
## Examples with complete.bg = TRUE
## Hence: the entire background set of the input ExpressionSet is considered
## when performing Fisher's exact test
# measure: log-foldchange
PlotEnrichment(ExpressionSet = PhyloExpressionSetExample,
test.set = test_set ,
legendName = "PS",
measure = "log-foldchange")
# measure: foldchange
PlotEnrichment(ExpressionSet = PhyloExpressionSetExample,
test.set = test_set ,
legendName = "PS",
measure = "foldchange")
## Examples with complete.bg = FALSE
## Hence: the test.set genes are excluded from the background set before
## Fisher's exact test is performed
# measure: log-foldchange
PlotEnrichment(ExpressionSet = PhyloExpressionSetExample,
test.set = test_set ,
complete.bg = FALSE,
legendName = "PS",
measure = "log-foldchange")
# measure: foldchange
PlotEnrichment(ExpressionSet = PhyloExpressionSetExample,
test.set = test_set ,
complete.bg = FALSE,
legendName = "PS",
measure = "foldchange")
# }
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