Issue176: fix filterFeatures() #177
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lgatto
reviewed
Oct 12, 2022
| @@ -309,6 +309,8 @@ filterFeaturesWithFormula <- function(object, filter, na.rm, keep, ...) { | |||
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| ## Internal function that | |||
| .checkFilterVariables <- function(object, vars) { | |||
| ## Ignore variables from the user environment | |||
| vars <- vars[!vars %in% ls(envir = parent.frame(4))] | |||
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What is this number 4 here? Is it always 4?
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Yes it is always four because we only want to include variables from the environment the function was called in (may not always be .GlobalEnv). Here is a "traceback" counter:
0 in .checkFilterVariables()
1 in FilterFeaturesWithFormula()
2 in .local()
3 in filterFeatures()
4 in environment the function was called
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I'm improving the unit test to ensure this is checked.
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Could you also add this information as a comment in the code.
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Pushed to Bioc |
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This PR should solve the issue highlighted in statOmics/msqrob2#42
There is also small code refactoring that will later be required for HDF5 support #171 (sorry for the leak).