Add documentation to functions, datasets, and add vignette
Closed this issue · 4 comments
Odd little chunk in the vignette pointed out by @kechrisk :
"Identifiers in the datasets - LCMS_Run_ID = operator/replicate (A-C), subject (01-03), concentration (1x,2x,4x) - SubjectID = subject (01-03), concentration (1x,2x,4x)"
Per @mmulvahill this is the beginning of documentation for the data set. I will either fully document or delete it.
I will fill in the final output section of the vignette once the print methods are up to date as specified in #21
In answer to a question from @kechrisk : the coefficient of variation cutoff in ms_prepare is given by the cvmax parameter, current default 0.5.
The line "a list of the column numbers containing them should be provided in the controls variable" in the vignette is ambiguous. @kechrisk notes, "The data is provided where compounds are rows, so what does column numbers mean here?" I think this means that if there are control subjects in the data set, a vector containing their indices should be passed as the controls argument. I will investigate and fix the documentation.