Output of vignette.

[tuh8888]

Addressed Katerina's suggestions

• Section 3

1) This may be a question more for Matt but the vignette is written expecting replciates/spike-in/batches. What if a user does not have replicates, spike-ins or batches? Can the package handle that? If so, we should show an example without that information.

• Leaving this for Matt or Daniel

2) I'm not sure what this section is, it seems repetitive

"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)"

• Removed

• Section 5

3) What is the default CV cutoff for the "ms_prepare" function? Is there an option in the function to change that value?

• Added description of the parameters.

• Section 7

4) For BPCA, are there any parameters for "ms_impute"? I think we should provide a quick description of parameters for each method (e.g., k for KNN), and then cite the other package.

• No parameters other than k for KNN are in the ms_impute() function. The parameters for the underlying impute functions should probably be allowed here too.

• I'll come back and add citations and parameter descriptions once we include them all.

5) What are the variables " n_comp = 2, n_control = 10" for ms_normalize? Are those specific to CRMN? Like above, I think we should provide a quick description of parameters for each method (e.g., k for KNN), and then cite the other package.

• Same as above. Parameter descriptions are in the function documentation. I'm not sure they also need to be in the vignette too.

• Section 8

6) What does this mean "a list of the column numbers containing them should be provided in the controls variable"? The data is provided where compounds are rows, so what does column numbers mean here?

• I guess these are actually samples? I can't tell if they are used as rows or columns. They are eventually passe to crmn:normalize as standards. It's hard to tell what they do from there.

• Section 9 7) The "Final output" section is empty

• Removed

[codecov[bot]]

Codecov Report

Merging #23 into master will not change coverage. The diff coverage is n/a.

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  Files           6        6           
  Lines         383      383           
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  Hits          191      191           
  Misses        192      192

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