sbpiper_sim: Main R function for SBpipe pipeline: simulate().

In pdp10/sbpiper: Data Analysis Functions for 'SBpipe' Package

Description

Main R function for SBpipe pipeline: simulate().

Usage

sbpiper_sim(model, inputdir, outputdir, outputfile_stats, outputfile_repeats,
  exp_dataset, plot_exp_dataset, exp_dataset_alpha, xaxis_label, yaxis_label,
  column_to_read)

Arguments

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

Examples

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")

pdp10/sbpiper documentation built on May 17, 2019, 11:17 p.m.