Description Usage Arguments Examples
Main R function for SBpipe pipeline: simulate().
1 2 3 | sbpiper_sim(model, inputdir, outputdir, outputfile_stats, outputfile_repeats,
exp_dataset, plot_exp_dataset, exp_dataset_alpha, xaxis_label, yaxis_label,
column_to_read)
|
model |
the model name |
inputdir |
the input directory |
outputdir |
the output directory |
outputfile_stats |
the output file containing the statistics |
outputfile_repeats |
the output file storing the model simulation repeats |
exp_dataset |
the file containing the experimental data. |
plot_exp_dataset |
TRUE if the experimental data should also be plotted |
exp_dataset_alpha |
the alpha level for the data set |
xaxis_label |
the label for the x axis (e.g. Time (min)) |
yaxis_label |
the label for the y axis (e.g. Level (a.u.)) |
column_to_read |
the name of the column to process |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | data(insulin_receptor_1)
data(insulin_receptor_2)
data(insulin_receptor_3)
data(insulin_receptor_exp_dataset)
dir.create(file.path("sim_datasets"))
dir.create(file.path("sim_datasets_sum"))
write.table(insulin_receptor_1,
file=file.path("sim_datasets", "insulin_receptor_1.csv"),
row.names=FALSE)
write.table(insulin_receptor_2,
file=file.path("sim_datasets", "insulin_receptor_2.csv"),
row.names=FALSE)
write.table(insulin_receptor_3,
file=file.path("sim_datasets", "insulin_receptor_3.csv"),
row.names=FALSE)
write.table(insulin_receptor_exp_dataset,
file="insulin_receptor_exp_dataset.csv",
row.names=FALSE)
sbpiper_sim(model="insulin_receptor",
inputdir="sim_datasets",
outputdir="sim_plots",
outputfile_stats="insulin_receptor_IR_beta_pY1146_stats.csv",
outputfile_repeats=file.path("sim_datasets_sum",
"insulin_receptor_IR_beta_pY1146.csv"),
exp_dataset="insulin_receptor_exp_dataset.csv",
plot_exp_dataset=TRUE,
exp_dataset_alpha=1.0,
xaxis_label=NULL,
yaxis_label=NULL,
column_to_read="IR_beta_pY1146")
|
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