Nothing
## ----echo = FALSE, message = FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
options(width = 750)
knitr::opts_chunk$set(
comment = "#>",
error = FALSE,
tidy = FALSE)
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # install myTAI
# install.packages("myTAI")
#
# # load myTAI
# library(myTAI)
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# library(readxl)
#
# # read expression data (organ specific genes) from Sestak and Domazet-Loso, 2015
# Drerio.OrganSpecificExpression <- read_excel("TableS3-2.xlsx", sheet = 2, skip = 3)
#
# # select only brain specific genes
# Drerio.Brain.Genes <- unlist(unique(na.omit(Drerio.OrganSpecificExpression[ , "brain"])))
#
# # visualize enriched Phylostrata of genes annotated as brain specific
# PlotEnrichment(Drerio.PhyloMap,
# test.set = Drerio.Brain.Genes,
# measure = "foldchange",
# use.only.map = TRUE,
# legendName = "PS")
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# BrainGenes <- SelectGeneSet(ExpressionSet = Drerio.PhyloMap,
# gene.set = Drerio.Brain.Genes,
# use.only.map = TRUE)
#
# # select only brain genes originating in PS5
# BrainGenes.PS5 <- BrainGenes[which(BrainGenes[ , "Phylostrata"] == 5), ]
#
# # look at the results
# head(BrainGenes.PS5)
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # find filter for zfin.org ids
# organismFilters("Danio rerio", topic = "zfin_id")
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # find go attribute term for D. rerio
# organismAttributes("Danio rerio", topic = "go")
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # retrieve GO terms of D. rerio brain genes originating in PS5
# GO_tbl.BrainGenes <- biomart(genes = unlist(BrainGenes.PS5[ , "ZFIN_ID"]),
# mart = "ENSEMBL_MART_ENSEMBL",
# dataset = "drerio_gene_ensembl",
# attributes = "go_id",
# filters = "zfin_id")
#
# head(GO_tbl.BrainGenes)
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