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gabrielodom / pathwayPCA

integrative pathway analysis with modern PCA methodology and gene selection
https://gabrielodom.github.io/pathwayPCA/
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Checking functions are called in CreateOmics*() instead of CreateOmics() #46

Closed gabrielodom closed 5 years ago

gabrielodom commented 5 years ago

Here's the issue: if I submit a "clean" assay, anyNA() returns FALSE. However, if one of the columns of the assay has variance near 0, then scaling (which happens in CreateOmics()) will create columns with NA values. Therefore, the user will get the error "Missing observations are not permitted in the assay data.", but they will have no missing values.

Solution: move the calls to CheckAssay() and CheckPwyColl() from the nested CreateOmics*() functions into the CreateOmics() wrapper.