Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----message= FALSE, warning=FALSE--------------------------------------------
library(ceRNAnetsim)
library(png)
## ---- message=FALSE, warning= FALSE, eval=FALSE-------------------------------
# if (!requireNamespace("BiocManager", quietly = TRUE))
# install.packages("BiocManager")
# BiocManager::install("ceRNAnetsim")
## ---- fig.height=5, fig.width=6, warning=FALSE, message=FALSE, fig.show='hide'----
data("minsamp")
minsamp %>%
priming_graph(competing_count = Competing_expression,
miRNA_count = miRNA_expression) %>%
update_how("Gene4",2) %>%
simulate_vis(title = "Minsamp: Common element as trigger", cycle = 15)
minsamp %>%
priming_graph(competing_count = Competing_expression,
miRNA_count = miRNA_expression) %>%
update_how("Gene4",2) %>%
simulate(cycle = 5)
## -----------------------------------------------------------------------------
data("midsamp")
midsamp
## ---- fig.height=5, fig.width=6, warning=FALSE, message=FALSE, fig.show='hide'----
midsamp %>%
priming_graph(Gene_expression, miRNA_expression) %>%
update_how("Gene17",2) %>%
simulate_vis(title = "Midsamp: Gene with higher degree as trigger", 15)
## -----------------------------------------------------------------------------
midsamp %>%
priming_graph(Gene_expression, miRNA_expression) %>%
update_how("Gene2",2) %>%
simulate(50) %>%
find_iteration(limit=0)
## -----------------------------------------------------------------------------
data("midsamp_new_counts")
midsamp %>%
priming_graph(Gene_expression, miRNA_expression) %>%
update_variables(current_counts = midsamp_new_counts) %>%
simulate(50) %>%
find_iteration(limit=0)
## ---- fig.align='center', fig.width=5, fig.height=3, dpi= 120-----------------
midsamp %>%
priming_graph(Gene_expression, miRNA_expression) %>%
update_how("Gene17",2) %>%
simulate(50) %>%
find_iteration(limit=0)
## ---- fig.height=5, fig.width=6, warning=FALSE, message=FALSE, fig.show='hide'----
midsamp %>%
priming_graph(Gene_expression, miRNA_expression) %>%
update_how("Gene17", 2) %>%
simulate_vis(title = "Midsamp: Gene17 2 fold increase, 25 cycles", 25)
## ---- fig.align='center', fig.height=5, fig.width=6, warning=FALSE, message=FALSE, fig.show='hide'----
midsamp %>%
priming_graph(Gene_expression, miRNA_expression) %>%
update_how("Gene17", 2) %>%
simulate_vis(title = "Midsamp: Gene17 2 fold increase, 6 cycles", 6, threshold = 1)
## -----------------------------------------------------------------------------
midsamp %>%
priming_graph(competing_count = Gene_expression,
miRNA_count = miRNA_expression,
aff_factor = c(Energy,seeds),
deg_factor = targeting_region) %>%
calc_perturbation("Gene17", 3, cycle = 30, limit = 0.1)
## -----------------------------------------------------------------------------
primed_mid <- midsamp %>%
priming_graph(competing_count = Gene_expression,
miRNA_count = miRNA_expression,
aff_factor = c(Energy,seeds),
deg_factor = targeting_region)
## ---- eval=FALSE--------------------------------------------------------------
# # for parallel processing
# # future::plan(multiprocess)
#
# seq(2,10) %>%
# rlang::set_names() %>%
# furrr::future_map_dfr(~ primed_mid %>% calc_perturbation("Gene17", .x, cycle = 30, limit = 0.1), .id="fold_change")
## ---- warning=FALSE-----------------------------------------------------------
midsamp %>%
priming_graph(competing_count = Gene_expression,
miRNA_count = miRNA_expression,
aff_factor = c(Energy,seeds),
deg_factor = targeting_region) %>%
find_node_perturbation(how = 3, cycle = 4, limit = 0.1)%>%
select(name, perturbation_efficiency, perturbed_count)
## -----------------------------------------------------------------------------
midsamp %>%
priming_graph(competing_count = Gene_expression,
miRNA_count = miRNA_expression,
aff_factor = c(Energy,seeds),
deg_factor = targeting_region) %>%
find_node_perturbation(how = 3, cycle = 4, limit = 0.1, fast=5)%>%
select(name, perturbation_efficiency, perturbed_count)
## ----sessioninfo--------------------------------------------------------------
sessionInfo()
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