Table 1 Genometric RGMQL functions with their extension over already existing R functions and mapping to corresponding GMQL operators
R package of origin | RGMQL function | GMQL operator | Brief description |
|---|---|---|---|
dplyr | arrange() | ORDER | It orders samples sample regions based on metadata region attributes |
dplyr | collect() | MATERIALIZE | Itsaves persistently the content of any dataset obtained after query completion |
dplyr | filter() | SELECT | It extracts a subset of samples sample regions using region metadata predicates |
dplyr | group_by() | GROUP | It groups samples sample regions based on region metadata attributes with the same value |
dplyr | select() | PROJECT | It selects region metadata attributes to be kept and can update create metadata region attributes |
dplyr | setdiff() | DIFFERENCE | It discards the regions of the first dataset intersecting regions of the second one |
dplyr | union() | UNION | It puts together samples of two datasets keeping as region attributes those of the first one |
base | merge() | JOIN | It returns a dataset by joining the regions of two datasets based on distance region predicates |
stats | aggregate() | MERGE | It combines all the samples of a dataset into a single sample |
– | cover() | COVER | It collapses the samples of a dataset into a single sample based on specified rules |
– | execute() | – | It launches the query execution |
– | extend() | EXTEND | It generates new metadata attributes for each sample from aggregations applied to region attributes |
– | map() | MAP | It computes aggregated values from overlapping regions of two datasets |