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Performs aggregation on metadata contained in the association file.

Source: R/aggregate-functions.R
aggregate_metadata.Rd

[Stable] Groups metadata by the specified grouping keys and returns a summary of info for each group. For more details on how to use this function: vignette("workflow_start", package = "ISAnalytics")

Usage

aggregate_metadata(
  association_file,
  grouping_keys = c("SubjectID", "CellMarker", "Tissue", "TimePoint"),
  aggregating_functions = default_meta_agg(),
  import_stats = lifecycle::deprecated()
)

Arguments

association_file

The imported association file (via import_association_file)

grouping_keys

A character vector of column names to form a grouping operation

aggregating_functions

A data frame containing specifications of the functions to be applied to columns in the association file during aggregation. It defaults to default_meta_agg. The structure of this data frame should be maintained if the user wishes to change the defaults.

import_stats

[Deprecated] The import of VISPA2 stats has been moved to its dedicated function, see import_Vispa2_stats.

Value

An aggregated data frame

See also

Other Data cleaning and pre-processing: aggregate_values_by_key(), compute_near_integrations(), default_meta_agg(), outlier_filter(), outliers_by_pool_fragments(), purity_filter(), realign_after_collisions(), remove_collisions(), threshold_filter()

Examples

data("association_file", package = "ISAnalytics")
aggreg_meta <- aggregate_metadata(
    association_file = association_file
)
head(aggreg_meta)
#> # A tibble: 6 × 19
#>   SubjectID CellMarker Tissue TimePoint FusionPrimerPCRDate_…¹ LinearPCRDate_min
#>   <chr>     <chr>      <chr>  <chr>     <date>                 <date>           
#> 1 PT001     MNC        BM     0030      2016-11-03             Inf              
#> 2 PT001     MNC        BM     0060      2016-11-03             Inf              
#> 3 PT001     MNC        BM     0090      2016-11-03             Inf              
#> 4 PT001     MNC        BM     0180      2016-11-03             Inf              
#> 5 PT001     MNC        BM     0360      2017-04-21             Inf              
#> 6 PT001     MNC        PB     0030      2016-11-03             Inf              
#> # ℹ abbreviated name: ¹​FusionPrimerPCRDate_min
#> # ℹ 13 more variables: VCN_avg <dbl>, `ng DNA corrected_avg` <dbl>,
#> #   Kapa_avg <dbl>, `ng DNA corrected_sum` <dbl>, ulForPool_sum <dbl>,
#> #   BARCODE_MUX_sum <int>, TRIMMING_FINAL_LTRLC_sum <int>, LV_MAPPED_sum <int>,
#> #   BWA_MAPPED_OVERALL_sum <int>, ISS_MAPPED_OVERALL_sum <int>,
#> #   PCRMethod <chr>, NGSTechnology <chr>, DNAnumber <chr>