# NOT RUN {
data(PhyloExpressionSetExample)
# remove genes that have an expression level below 8000
# in at least one developmental stage
FilterConst <- Expressed(ExpressionSet = PhyloExpressionSetExample,
cut.off = 8000,
method = "const",
comparison = "below")
dim(FilterConst) # check number of retained genes
# remove genes that have an expression level below 8000
# in at least 3 developmental stages
# (in this case: ceiling(7/2) = 4 stages fulfilling the cut-off criteria)
FilterMinSet <- Expressed(ExpressionSet = PhyloExpressionSetExample,
cut.off = 8000,
method = "min-set",
comparison = "below")
dim(FilterMinSet) # check number of retained genes
# remove genes that have an expression level below 8000
# in at least 5 developmental stages (in this case: n = 2 stages fulfilling the criteria)
FilterNSet <- Expressed(ExpressionSet = PhyloExpressionSetExample,
cut.off = 8000,
method = "n-set",
comparison = "below",
n = 2)
dim(FilterMinSet) # check number of retained genes
# remove expression levels that exceed the cut.off criteria
FilterMinSet <- Expressed(ExpressionSet = PhyloExpressionSetExample,
cut.off = 12000,
method = "min-set",
comparison = "above")
dim(FilterMinSet) # check number of retained genes
# remove expression levels that undercut AND exceed the cut.off criteria
FilterMinSet <- Expressed(ExpressionSet = PhyloExpressionSetExample,
cut.off = c(8000,12000),
method = "min-set",
comparison = "both")
dim(FilterMinSet) # check number of retained genes
# }
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