Nothing
## ----setup, include = FALSE----------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
echo = TRUE,
fig.align = "center",
eval = F
)
## ---- eval = F-----------------------------------------------------------
# install.packages("sismonr")
## ------------------------------------------------------------------------
# library(sismonr)
## ------------------------------------------------------------------------
# myinsilicosystem = createInSilicoSystem(G = 10, PC.p = 0.7, ploidy = 2)
## ---- eval = F-----------------------------------------------------------
# ?insilicosystemargs
## ------------------------------------------------------------------------
# class(myinsilicosystem)
# names(myinsilicosystem)
## ------------------------------------------------------------------------
# myinsilicosystem$genes
## ------------------------------------------------------------------------
# ## system with only protein-coding genes, all regulators of transcription (PC.TC.p),
# ## and all regulations are activations (positive regulation - TC.pos.p)
# myinsilicosystem2 = createInSilicoSystem(G = 15, PC.p = 1, PC.TC.p = 1, TC.pos.p = 1)
# myinsilicosystem2$genes
#
# ## Changing the function used to sample transcription rates for the genes
# myinsilicosystem3 = createInSilicoSystem(G = 10,
# basal_transcription_rate_samplingfct = function(x){runif(x, 0.1, 0.8)})
# myinsilicosystem3$genes
## ------------------------------------------------------------------------
# myinsilicosystem$edg
## ------------------------------------------------------------------------
# myinsilicosystem$complexes
# myinsilicosystem$complexeskinetics
## ------------------------------------------------------------------------
# myinsilicosystem$complexesTargetReaction
## ---- fig.width = 6, fig.height = 6--------------------------------------
# plotGRN(myinsilicosystem)
## ---- fig.width = 6, fig.height = 6--------------------------------------
# plotGRN(myinsilicosystem, edgeType = "TC")
## ------------------------------------------------------------------------
# names(myinsilicosystem$mosystem)
# myinsilicosystem$mosystem$TCRN_edg
## ------------------------------------------------------------------------
# myinsilicosystem$mosystem$TLRN_edg
# myinsilicosystem$mosystem$RDRN_edg
# myinsilicosystem$mosystem$PDRN_edg
# myinsilicosystem$mosystem$PTMRN_edg
## ------------------------------------------------------------------------
# mypop = createInSilicoPopulation(3, myinsilicosystem, ngenevariants = 4)
## ---- eval = F-----------------------------------------------------------
# ?insilicoindividualargs
## ------------------------------------------------------------------------
# class(mypop)
# names(mypop)
## ------------------------------------------------------------------------
# mypop$GenesVariants
## ------------------------------------------------------------------------
# mypop2 = createInSilicoPopulation(3, myinsilicosystem, ngenevariants = 2)
# mypop2$GenesVariants
#
# ## Creating a smaller system with only 3 genes
# mysystem = createInSilicoSystem(G = 3, PC.p = 1)
#
# ## We will create only 1 variant of gene 1, 3 variants of gene 2 and
# ## 2 variants of gene 3
# nbvariants = c(1, 3, 2)
#
# qtlnames = c("qtlTCrate", "qtlRDrate",
# "qtlTCregbind", "qtlRDregrate",
# "qtlactivity", "qtlTLrate",
# "qtlPDrate", "qtlTLregbind",
# "qtlPDregrate", "qtlPTMregrate")
#
# genvariants = lapply(nbvariants, function(x){
# matrix(1, nrow = length(qtlnames), ncol = x,
# dimnames = list(qtlnames, 1:x))
# })
# names(genvariants) = mysystem$genes$id
#
# ## the 2nd variant of gene 2 has a mutation reducing its transcription rate by 3
# genvariants$`2`["qtlTCrate", 2] = 0.33
# ## and the 3rd variant has an increased translation rate
# genvariants$`2`["qtlTLrate", 2] = 1.5
#
# ## The 2nd variant of gene 3 has a mutation decreasing the activity of
# ## its active product
# genvariants$`3`["qtlactivity", 2] = 0.7
#
# ## Allelic frequency of each variant
# genvariants.freq = list('1' = c(1),
# '2' = c(0.6, 0.3, 0.1),
# '3' = c(0.9, 0.1))
#
# mypop3 = createInSilicoPopulation(10, mysystem,
# genvariants = genvariants,
# genvariants.freq = genvariants.freq)
## ------------------------------------------------------------------------
# names(mypop$individualsList)
## ------------------------------------------------------------------------
# mypop$individualsList$Ind1$haplotype
# mypop$individualsList$Ind2$haplotype
# mypop$individualsList$Ind3$haplotype
## ---- fig.width = 7, fig.height = 6--------------------------------------
# plotMutations(mypop, myinsilicosystem, nGenesPerRow = 5)
## ---- fig.width = 6, fig.height = 6--------------------------------------
# plotMutations(mypop, myinsilicosystem,
# qtlEffectCoeffs = c("qtlTCrate", "qtlTLrate", "qtlRDrate", "qtlPDrate"),
# inds = c("Ind1", "Ind2"),
# alleles = "GCN2",
# genes = 1:3)
## ------------------------------------------------------------------------
# sim = simulateInSilicoSystem(myinsilicosystem, mypop, simtime = 1000, ntrials = 5)
## ------------------------------------------------------------------------
# sim = simulateParallelInSilicoSystem(myinsilicosystem, mypop, simtime = 1000, ntrials = 5)
## ------------------------------------------------------------------------
# sim$runningtime
## ------------------------------------------------------------------------
# head(sim$Simulation)
## ---- fig.width = 7, fig.height = 6--------------------------------------
# plotSimulation(sim$Simulation)
## ---- eval = F-----------------------------------------------------------
# plotSimulation(sim$Simulation, yLogScale = F)
## ---- eval = F-----------------------------------------------------------
# plotSimulation(sim$Simulation, inds = c("Ind1"), timeMin = 200, timeMax = 300)
## ---- fig.width = 6.5, fig.height = 6------------------------------------
# plotHeatMap(sim$Simulation)
## ------------------------------------------------------------------------
# simNoAllele = mergeAlleleAbundance(sim$Simulation)
# head(simNoAllele)
## ------------------------------------------------------------------------
# simNoPTM = mergePTMAbundance(simNoAllele)
# head(simNoPTM)
## ------------------------------------------------------------------------
# simNoComplex = mergeComplexesAbundance(simNoAllele)
# head(simNoComplex)
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