Nothing
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # read expression data (organ specific genes) from Sestak and Domazet-Loso, 2015
# Drerio.OrganSpecificExpression <- read_excel("MBE_2015a_Drerio_PhyloMap.xlsx", sheet = 2, skip = 3)
#
# # select only brain specific genes
# Drerio.Brain.Genes <- unique(na.omit(Drerio.OrganSpecificExpression[ , "brain"]))
#
# # visualize enriched Phylostrata of genes annotated as brain specific
# PlotEnrichment(Drerio.PhyloMap,
# test.set = Drerio.Brain.Genes,
# measure = "log-foldchange",
# use.only.map = TRUE,
# legendName = "PS")
#
## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# PlotEnrichment(Drerio.PhyloMap,
# test.set = Drerio.Brain.Genes,
# measure = "log-foldchange",
# use.only.map = TRUE,
# legendName = "PS")
## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # specify plot.bars = FALSE to retrieve only numeric results
# EnrichmentResult <- PlotEnrichment(Drerio.PhyloMap,
# test.set = Drerio.Brain.Genes,
# measure = "log-foldchange",
# use.only.map = TRUE,
# legendName = "PS",
# plot.bars = FALSE)
#
# # access p-values quantifying the enrichment for each Phylostratum
# EnrichmentResult$p.values
## ---- eval = FALSE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # access enrichment matrix storing C_1 and C_2
# EnrichmentResult$enrichment.matrix
#
## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # complete.bg = TRUE (default) -> retain test.set genes in background set
# PlotEnrichment(Drerio.PhyloMap,
# test.set = Drerio.Brain.Genes,
# measure = "log-foldchange",
# complete.bg = TRUE,
# use.only.map = TRUE,
# legendName = "PS")
## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # complete.bg = FALSE -> remove test.set genes from background set
# PlotEnrichment(Drerio.PhyloMap,
# test.set = Drerio.Brain.Genes,
# measure = "log-foldchange",
# complete.bg = FALSE,
# use.only.map = TRUE,
# legendName = "PS")
## ---- eval = FALSE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# PlotEnrichment(Drerio.PhyloMap,
# test.set = Drerio.Brain.Genes,
# measure = "foldchange",
# complete.bg = TRUE,
# use.only.map = TRUE,
# legendName = "PS")
## ---- eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # retrieve the taxonomy of D. rerio
# taxonomy(organism = "Danio rerio")
## ---- eval = FALSE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # the best parameter setting to visualize this plot:
# # png("DrerioBrainSpecificGeneExpression.png",700,400)
# PlotGeneSet(ExpressionSet = DrerioPhyloExpressionSet,
# gene.set = Drerio.Brain.Genes,
# plot.legend = FALSE,
# type = "l",
# lty = 1,
# lwd = 4,
# xlab = "Ontogeny",
# ylab = "Expression Level")
#
# # dev.off()
## ---- eval = FALSE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # select the ExpressionSet subset of Brain specific genes
# Brain.PhyloExpressionSet <- SelectGeneSet( ExpressionSet = DrerioPhyloExpressionSet,
# gene.set = Drerio.Brain.Genes )
#
# head(Brain.PhyloExpressionSet)
## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # adjust p-values for multiple comparisons with Benjamini & Hochberg (1995)
# PlotEnrichment(Drerio.PhyloMap,
# test.set = Drerio.Brain.Genes,
# measure = "log-foldchange",
# complete.bg = FALSE,
# use.only.map = TRUE,
# legendName = "PS",
# p.adjust.method = "BH")
#
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