getID: Pulls IDs from the metabolite files and optionally write to a...
In buddha2490/BERGMets: Metabolomics data and analysis in the BERG

Description Usage Arguments Details Value Author(s) See Also Examples

Each metabolite has an ID file. The getID() function will pull these IDs. By default, getID() will create a data frame in your global environment. You can also request export to SAS via the foreign:: package. See details.

1	getID(dat,filepath=NULL)

`dat`	Character vector of the dataset you are requesting (see details below). Options are NOT case sensitive.
`filepath`	Optional file path to save the ID file. Remember that R requires forward slashes "/" in file paths. Example: "S:/user/bcarter/" NOT "S:\user\bcarter". If you leave filepath=NULL, getID() will simply create an ID file within your global environment.

Users can pull IDs from any of 7 metabolomics projects using the following character strings. For more information, you can find documentation by searching the BERGMets documentation

SAS foreign files: The foreign package does two things. First, it creates a .txt file of the data you are exporting from R. Second, it writes a SAS program that will import this .txt file into SAS and format everything correctly. Selecting this option will write a data file and a .SAS program to your filepath. Simply run the SAS program and your data will be imported.

getID() will only return a data frame named "Metabolomics_IDs" if you leave filepath=NULL. Otherwise, it will save an .xpt or .txt/.sas files to your filepath. You can move on to SAS to finish your analysis.

Brian Carter

getMetabolites

# Pull the IDs for use in R

# Will return a data frame named "Metabolomics_IDs"

getID("breast_metabolomics")


# Export to SAS using the foreign package

# Creates 2 files:

  # "Import ID_Breast_metabolomics.SAS"

  # "ID_breast_metabolomics"

# Simply run the "Import ID_Breast_metabolomics.SAS" and continue in SAS

  getID(dat="breast_metabolomics",
        filepath="S:/user/bcarter/metabolites")