Beginning of making filtering steps all work together #41
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cansavvy
reviewed
Jul 1, 2024
| #TRUE means it should be filtered, FALSE means it shouldn't be filtered | ||
| combined_filter <- rowSums(reduce(possible_filters, cbind)) >= min_n_filters | ||
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| gimap_dataset$filtered <- NULL #TODO: Filtered version of the data can be stored here |
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Add here a nice readable version of combined_filter to gimap_dataset and then the filtered version of the data to filtered_data
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This is in a later PR so I think this means this is set to go!
cansavvy
approved these changes
Jul 3, 2024
| @@ -18,18 +23,57 @@ | |||
| #' | |||
| #' # To see filtered data | |||
| #' gimap_dataset$filtered_data | |||
| #' | |||
| #' # If you want to only use a single filter or some subset, specify which using the filter_type parameter | |||
| #' gimap_dataset <- gimap_filter(gimap_dataset, filter_type = "zero_count_only") | |||
| #TRUE means it should be filtered, FALSE means it shouldn't be filtered | ||
| combined_filter <- rowSums(reduce(possible_filters, cbind)) >= min_n_filters | ||
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| gimap_dataset$filtered <- NULL #TODO: Filtered version of the data can be stored here |
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This is in a later PR so I think this means this is set to go!
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Sorry, this PR is the first step of filtering where the
filter_kibranch builds on thefilter_qc_ki5branch. PR #40 is trying to mergefilter_ki2intofilter_ki. I submitted those PRs out of order since this one will be PR #41.This PR makes a lot of documentation changes, explaining parameters and how to use the
gimap_filter()function.It also builds the groundwork for the filters working together.
reduce()function tocbindthese filters together. This approach ignores NULLs and returns a df with column(s) of TRUEs and FALSEs.min_n_filtersparameter is used together withrowSumsto find out which pgRNA constructs are flagged by at least that minimum number of filters that would result in the pgRNA constructs being removed from the dataset -- creating a consensus or combined filter.