Name Mode Size
ConnectedComponent-class.R 100644 14 kb
PSM-class.R 100644 14 kb
PSM-filter.R 100644 4 kb
PSM-read.R 100644 1 kb
PSM-reduce.R 100644 1 kb
PSMatch-package.R 100644 3 kb
adjacencyMatrix-accessors.R 100644 1 kb
adjacencyMatrix-create.R 100644 12 kb
adjacencyMatrix-plot.R 100644 5 kb
describe.R 100644 4 kb
fragments-add.R 100644 4 kb
fragments-calculate.R 100644 12 kb
fragments-utils.R 100644 4 kb
functions-mzR.R 100644 4 kb
# Handling peptide-spectrum matches `PSMatch` is a simple package to load, process and analyse PSMs (Peptide-Spectrum Matches). The following references are a good way to get started with the package: - The [package manual package]( for a general overview of the main concepts tackled by the `PSMatch` package. - The [Working with PSM data]( vignette to learn about the `PSM` to read and filter peptide-spectrum matches. - The [Understanding protein groups with adjacency matrices]( vignette to learn about adjaceny matrices and connected components to explore and manage protein groups. - The [MS2 fragment ions]( vignette to calculate and visualise MS2 fragment ions. ## Installation instructions To install the package from Bioconductor, make sure you have the `BiocManager` package, available from CRAN, and then run ```r BiocManager::install("PSMatch") ``` ## Credit Code in this package is partly composed of functions ported from [`MSnbase`]( with the goal to (1) make them more general and (2) integrate them with the [*R for Mass Spectrometry*]( infrastructure.