createComplist: Wrapper Function To Create A Complist Object from Scratch

In thomasp85/pepmaps: Create peptide maps by merging xcms (and CAMERA) with MassAI

Description

This function guides the user through the creation of a Complist object. It handles all xcms and CAMERA function calls as well as the pepmaps calls.

Usage

createComplist(mzXML, Sample.info, ID = "MassAI", par = "standard", sep = "\t", dec = ".", annotate = TRUE)

Arguments

mzXML	The path to the folder containing the .mzXML files used for the analysis. If missing the function lets you choose a folder.
Sample.info	A data frame containing information about the samples arranged in alphabetical order to match the order of the .mzXML files. (optional)
ID	The type of identification carried out (only 'MassAI' supported at the moment).
par	The name of the parameter set used for the analysis.
sep	The seperator used in the ID file.
dec	The decimal seperator used in the ID file
annotate	Logical. Should CAMERA annotation be carried out.

Details

This function conveniently handles all function calls necessary to create a Complist object. In it's barebone form only 'par' should be specified (except when using default values) making the function call: ans <- createComplist(par='name') sufficient. Under these circumstances the function directs the user to choosing the location of the .mzXML and ID files and outputs a Complist object.

Value

A Complist object.

Author(s)

Thomas Dybdal Pedersen

See Also

\listS4class{Complist}, complist, peaklist, pepID, Parameters

thomasp85/pepmaps documentation built on May 31, 2019, 11:15 a.m.