Table 1 Overview of the plyranges grammar
Verb | Description | |
|---|---|---|
Aggregate | summarize() | Aggregate over column(s) |
disjoin_ranges() | Aggregate column(s) over the union of end coordinates | |
reduce_ranges() | Aggregate column(s) by merging overlapping and neighboring ranges | |
Modify (Unary) | mutate() | Modifies any column |
select() | Select columns | |
arrange() | Sort by columns | |
stretch() | Extend range by fixed amount | |
shift_(direction) | Shift coordinates | |
flank_(direction) | Generate flanking regions | |
%intersection% | Row-wise intersection | |
%union% | Row-wise union | |
compute_coverage | Coverage over all ranges | |
Modify (Binary) | %setdiff% | Row-wise set difference |
between() | Row-wise gap range | |
span() | Row-wise spanning range | |
Merge | join_overlap_*() | Merge by overlapping ranges |
join_nearest | Merge by nearest neighbor ranges | |
join_follow | Merge by following ranges | |
join_precedes | Merge by preceding ranges | |
union_ranges | Range-wise union | |
intersect_ranges | Range-wise intersect | |
setdiff_ranges | Range-wise set difference | |
complement_ranges | Range-wise set complement | |
Operate | anchor_direction() | Fix coordinates at direction |
group_by() | Partition by column(s) | |
group_by_overlaps() | Partition by overlaps | |
Restrict | filter() | Subset rows |
filter_by_overlaps() | Subset by overlap | |
filter_by_non_overlaps() | Subset by no overlap |