subMALDI is an open framework package for the R programming environment that permits organization, pre-processing (smoothing, baseline correction, peak detection), and normalization of spectral data sets. As a result of the package’s design, subMALDI data objects are compatible with functions from a wide variety of other R packages, and user-defined functions are easier to implement and test.
Installing in R
To install this package in R, begin by downloading the source copy of the package from the releases folder and install it using type = “source”. But, before you do this, a dependency from the BioConductor project is required. Begin by installing the BioConductor Manager:
and then install the package MassSpecWavelet:
Then install the CRAN-supported packages required:
Once the packages are all installed, you can then install the package:
Update the file name as necessary to whatever the copy you downloaded was set to for versioning.
Note: if you install from source, and set dependencies = TRUE, this should all be moot. This assumes you run the commands exactly as given, in which case, the BioConductor sequence doesn’t always seem to work. For example,
Getting Started
Refer to the vignette on workflow for a brief summary of the package functionality, and the vignette on processing for a simple example.
Contributing?
Examine our contribution guidelines for more.