Installation

To install MIMP, first make sure your R version is at least R 3.0. You can check by typing the following into your R console:

R.Version()$major

Next, install and load devtools package:

install.packages("devtools")
library("devtools")

Then install and load MIMP package from github:

install_github("MIMP", "omarwagih")
library("MIMP")

Running MIMP on sample data:

To start using MIMP, try loading paths to the sample data, which comes with the package:

# Get the path to example mutation data 
mut.file = system.file("extdata", "mutation_data.txt", package = "MIMP")

# Get the path to example FASTA sequence data 
seq.file = system.file("extdata", "sequence_data", package = "MIMP")

To take a look at the sample data, try running the following:

browseURL(mut.file)
browseURL(seq.file)

Now to start the analysis, simply run the mimp function on these files:

# Run rewiring analysis
results = mimp(mut.file, seq.file, display.results=TRUE)

The output is stored in the results variable and should show up in your browser. To suppress browser display, set display.results=FALSE

If you'd like to redisplay the results in your browser at a later time, run the following:

results2html(results)

Documentation

For a full list of all options, take a look at the documentation by typing the following in your R console:

?mimp