Add pre-processing vignette, new preProcessAdat() function
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- added pre-processing.Rmd to vignettes/articles/ with outline of topics to include - added entry to _pkgdown.yml
- drafted sections on filtering features, filtering samples, data qc and transformations - added `calcOutlierMap()` and its print and plot S3 methods, along with `getFlaggedIds()` for identifying sample level outliers
- added new function `preProcessAdat()` to filter features, filter samples, generate data qc plots, and perform standard analyte RFU transformations
- added comments to clarify filepath input to `read_adat()` example in README
- updated stat workflow articles with comments about how to read in the `example_data.adat` object - updated data preparation chunks to use the `preProcessAdat()` function for filtering features, filtering samples, data qc plots for covariate, and log10, center and scale transformations
- added snapshot unit tests for preProcessAdat() messaging, print and qc plot output - added helper utility functions for saving plot snapshot output to testthat/helper.R
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Pre-Processing and Documentation Updates
calcOutlierMap()and its print and plot S3 methods fromSomaPlotrpackage, along withgetFlaggedIds()for identifying sample level outlierspreProcessAdat()function which performs steps outlined in vignette, also now used in stat workflow articlestestthat/helper.RforpreProcessAdat()unit tests