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Revert metadata filtering in data_functions.R #176

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Nov 28, 2023
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Revert metadata filtering in data_functions.R #176

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11 changes: 8 additions & 3 deletions scripts/data_functions.R
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Original file line number Diff line number Diff line change
Expand Up @@ -130,8 +130,13 @@ subset_metadata <- function(exp_metadata, design, contrasts, current_facet, curr
contrasts_subset <- contrasts_subset %>% dplyr::filter(V2 %in% contrasts_to_filter)
}
exp_metadata_subset <- exp_metadata %>%
dplyr::filter(!!sym(design) %in% (unlist(contrasts_subset) %>% unique()) ) %>%
dplyr::filter(!!sym(current_facet) %in% current_filter)
dplyr::filter(!!sym(design) %in% (unlist(contrasts_subset) %>% unique()) ) # %>%
# dplyr::filter(!!sym(current_facet) %in% current_filter)
# The line above was added to deal with an edge case where samples were not properly filtered because current_facet wasn't in the contrast names
# That edge case is uncommon and there are probably easier ways to deal with it
# Including the commented dplyr code above breaks the analysis if controls aren't matched by chemical name
# Ex. works for BPA_10 vs BPA_0 (as in test data), but not for BPA_10 vs DMSO

# relevel the design and interesting groups
exp_metadata_subset[[design]] <- factor(exp_metadata_subset[[design]],
levels = unique(unlist(contrasts_subset)),
Expand Down Expand Up @@ -166,4 +171,4 @@ subset_results <- function(res, exp_metadata){
res_subset <- res[,exp_metadata_sorted$original_names]
return(res_subset)

}
}
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