extractMS: Extract embedded mass spectrometry data
In dpritchLibre/Bioactivity: PepSAVI-MS Data Analysis

Description Usage Arguments Details Value

Extract mass spectrometry data from an object with class binMS, class filterMS, or class msDat.

1	extractMS(msObj, type = "matrix")

`msObj`	An an object with class `binMS`, class `filterMS`, or class `msDat`.
`type`	A character string with value either "matrix", or "msDat". If "matrix" is provided as the argument, then the mass-to-charge values, charge values, and mass spectrometry data are combined into a single matrix and returned. If "msDat" is provided as the argument, then an `msDat` object containing this data is returned.

A convenience function for extracting and inspecting the mass spectrometry data in a binMS, filterMS, or msDat object. binMS and filterMS objects are lists that contain an msDat object, and specifying "msDat" for type merely returns the msDat element from the list for these classes of object. specifying "msDat" for an object with class "msDat" merely returns the argument, i.e. is the identity function. When "matrix" is specified, then the elements in the embedded msDat object are combined into a single matrix using cbind and returned.

Returns either a matrix containing the mass spectrometry data if "matrix" is specified as the argument to type, or an object with class msDat if "msDat" is specified as the argument to type. See Details for more detail regarding the return objects.