create_msnset.Rmd

# MSnSet Objects {#msnset-objects}

(See ?MSnbase::\`MSnSet-class\` for more details, as well as useful functions for modifying MSnSets and creating plots.)

An MSnSet is a convenient way to store MS proteomics expression and meta data in one object. It can be constructed with the `MSnbase::MSnSet` function, which accepts three arguments: 

1) `exprs` - a `matrix` of expression data with features as row names and samples as column names.
2) `fData` - a `data.frame` with features as row names (in the same order as the rows of `exprs`) and columns that describe each feature. This is not always necessary to include, but it is useful to store different feature IDs such as gene symbols.
3) `pData` - a `data.frame` with samples as row names (in the same order as the columns of `exprs`) and columns that describe each sample. This is almost always created from existing sample meta-data.