A fluent interface for manipulating GenomicRanges
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Documentation for package ‘plyranges’ version 1.18.0
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A B C D E F G I J M N O P R S T U W misc
| plyranges-package | plyranges: a grammar of genomic data manipulation |
-- A --
| add_nearest_distance | Add distance to nearest neighbours between two Ranges objects |
| add_nearest_distance_downstream | Add distance to nearest neighbours between two Ranges objects |
| add_nearest_distance_left | Add distance to nearest neighbours between two Ranges objects |
| add_nearest_distance_right | Add distance to nearest neighbours between two Ranges objects |
| add_nearest_distance_upstream | Add distance to nearest neighbours between two Ranges objects |
| anchor | Anchored Ranges objects |
| anchor_3p | Anchored Ranges objects |
| anchor_5p | Anchored Ranges objects |
| anchor_center | Anchored Ranges objects |
| anchor_centre | Anchored Ranges objects |
| anchor_end | Anchored Ranges objects |
| anchor_start | Anchored Ranges objects |
| arrange.Ranges | Sort a Ranges object |
| as_granges | Construct a I/GRanges object from a tibble or data.frame |
| as_iranges | Construct a I/GRanges object from a tibble or data.frame |
| as_ranges | Coerce an Rle or RleList object to Ranges |
-- B --
| BamFileOperator-class | An abstract class to represent operations performed over a file |
| between | Row-wise set operations on Ranges objects |
| bind_ranges | Combine Ranges by concatentating them together |
-- C --
| chop_by_gaps | Group a GRanges object by introns or gaps |
| chop_by_introns | Group a GRanges object by introns or gaps |
| complement_ranges | Vector-wise Range set-operations |
| complement_ranges_directed | Vector-wise Range set-operations |
| compute_coverage | Compute coverage over a Ranges object |
| count_overlaps | Count the number of overlaps between two Ranges objects |
| count_overlaps.GenomicRanges | Count the number of overlaps between two Ranges objects |
| count_overlaps.IntegerRanges | Count the number of overlaps between two Ranges objects |
| count_overlaps_directed | Count the number of overlaps between two Ranges objects |
| count_overlaps_directed.GenomicRanges | Count the number of overlaps between two Ranges objects |
| count_overlaps_within | Count the number of overlaps between two Ranges objects |
| count_overlaps_within.GenomicRanges | Count the number of overlaps between two Ranges objects |
| count_overlaps_within.IntegerRanges | Count the number of overlaps between two Ranges objects |
| count_overlaps_within_directed | Count the number of overlaps between two Ranges objects |
| count_overlaps_within_directed.GenomicRanges | Count the number of overlaps between two Ranges objects |
-- D --
| DeferredGenomicRanges-class | DeferredGenomiRanges objects |
| disjoin_ranges | Disjoin then aggregate a Ranges object |
| disjoin_ranges_directed | Disjoin then aggregate a Ranges object |
-- E --
| expand_ranges | Expand list-columns in a Ranges object |
-- F --
| FileOperator-class | An abstract class to represent operations performed over a file |
| filter-ranges | Subset a 'Ranges' object |
| filter.Ranges | Subset a 'Ranges' object |
| filter_by_non_overlaps | Filter by overlapping/non-overlapping ranges |
| filter_by_overlaps | Filter by overlapping/non-overlapping ranges |
| find_overlaps | Find overlap between two Ranges |
| find_overlaps.GenomicRanges | Find overlap between two Ranges |
| find_overlaps.IntegerRanges | Find overlap between two Ranges |
| find_overlaps_directed | Find overlap between two Ranges |
| find_overlaps_directed.GenomicRanges | Find overlap between two Ranges |
| find_overlaps_within | Find overlap between two Ranges |
| find_overlaps_within.GenomicRanges | Find overlap between two Ranges |
| find_overlaps_within.IntegerRanges | Find overlap between two Ranges |
| find_overlaps_within_directed | Find overlap between two Ranges |
| find_overlaps_within_directed.GenomicRanges | Find overlap between two Ranges |
| flank_downstream | Generate flanking regions |
| flank_left | Generate flanking regions |
| flank_right | Generate flanking regions |
| flank_upstream | Generate flanking regions |
-- G --
| genome_info | Construct annotation information |
| get_genome_info | Construct annotation information |
| GroupedGenomicRanges-class | Group a Ranges by one or more variables |
| GroupedIntegerRanges-class | Group a Ranges by one or more variables |
| groups.GroupedGenomicRanges | Group a Ranges by one or more variables |
| groups.GroupedIntegerRanges | Group a Ranges by one or more variables |
| group_by-ranges | Group a Ranges by one or more variables |
| group_by.GenomicRanges | Group a Ranges by one or more variables |
| group_by_overlaps | Find overlap between two Ranges |
| group_by_overlaps.GenomicRanges | Find overlap between two Ranges |
| group_by_overlaps.IntegerRanges | Find overlap between two Ranges |
-- I --
| id_to_column | Tools for working with named Ranges |
| intersect_ranges | Vector-wise Range set-operations |
| intersect_ranges_directed | Vector-wise Range set-operations |
| interweave | Interweave a pair of Ranges objects together |
-- J --
| join_follow | Find following Ranges |
| join_follow_left | Find following Ranges |
| join_follow_upstream | Find following Ranges |
| join_nearest | Find nearest neighbours between two Ranges objects |
| join_nearest_downstream | Find nearest neighbours between two Ranges objects |
| join_nearest_left | Find nearest neighbours between two Ranges objects |
| join_nearest_right | Find nearest neighbours between two Ranges objects |
| join_nearest_upstream | Find nearest neighbours between two Ranges objects |
| join_overlap_inner | Join by overlapping Ranges |
| join_overlap_inner_directed | Join by overlapping Ranges |
| join_overlap_inner_within | Join by overlapping Ranges |
| join_overlap_inner_within_directed | Join by overlapping Ranges |
| join_overlap_intersect | Join by overlapping Ranges |
| join_overlap_intersect_directed | Join by overlapping Ranges |
| join_overlap_intersect_within | Join by overlapping Ranges |
| join_overlap_intersect_within_directed | Join by overlapping Ranges |
| join_overlap_left | Join by overlapping Ranges |
| join_overlap_left_directed | Join by overlapping Ranges |
| join_overlap_left_within | Join by overlapping Ranges |
| join_overlap_left_within_directed | Join by overlapping Ranges |
| join_overlap_self | Find overlaps within a Ranges object |
| join_overlap_self_directed | Find overlaps within a Ranges object |
| join_overlap_self_within | Find overlaps within a Ranges object |
| join_overlap_self_within_directed | Find overlaps within a Ranges object |
| join_precede | Find preceding Ranges |
| join_precede_downstream | Find preceding Ranges |
| join_precede_right | Find preceding Ranges |
-- M --
| mutate.Ranges | Modify a Ranges object |
-- N --
| n | Compute the number of ranges in each group. |
| names_to_column | Tools for working with named Ranges |
| n_distinct | Compute the number of distinct unique values in a vector or List |
-- O --
| overscope_ranges | Create an overscoped environment from a Ranges object |
-- P --
| pair_follow | Pair together two ranges objects |
| pair_nearest | Pair together two ranges objects |
| pair_overlaps | Pair together two ranges objects |
| pair_precede | Pair together two ranges objects |
| plyranges | plyranges: a grammar of genomic data manipulation |
-- R --
| ranges-info | Construct annotation information |
| read_bam | Read a BAM file |
| read_bed | Read a BED or BEDGraph file |
| read_bed_graph | Read a BED or BEDGraph file |
| read_bigwig | Read a BigWig file |
| read_gff | Read a GFF/GTF/GVT file |
| read_gff1 | Read a GFF/GTF/GVT file |
| read_gff2 | Read a GFF/GTF/GVT file |
| read_gff3 | Read a GFF/GTF/GVT file |
| read_narrowpeaks | Read a BED or BEDGraph file |
| read_wig | Read a WIG file |
| reduce_ranges | Reduce then aggregate a Ranges object |
| reduce_ranges_directed | Reduce then aggregate a Ranges object |
| remove_names | Tools for working with named Ranges |
-- S --
| select.Ranges | Select metadata columns of the Ranges object by name or position |
| setdiff_ranges | Vector-wise Range set-operations |
| setdiff_ranges_directed | Vector-wise Range set-operations |
| set_end | Functional setters for Ranges objects |
| set_genome_info | Construct annotation information |
| set_seqnames | Functional setters for Ranges objects |
| set_start | Functional setters for Ranges objects |
| set_strand | Functional setters for Ranges objects |
| set_width | Functional setters for Ranges objects |
| shift_downstream | Shift all coordinates in a genomic interval left or right, upstream or downstream |
| shift_left | Shift all coordinates in a genomic interval left or right, upstream or downstream |
| shift_right | Shift all coordinates in a genomic interval left or right, upstream or downstream |
| shift_upstream | Shift all coordinates in a genomic interval left or right, upstream or downstream |
| slice.GroupedGenomicRanges | Choose rows by their position |
| slice.GroupedIntegerRanges | Choose rows by their position |
| slice.Ranges | Choose rows by their position |
| slide_ranges | Slide or tile over a Ranges object |
| span | Row-wise set operations on Ranges objects |
| stretch | Stretch a genomic interval |
| summarise.Ranges | Reduce multiple values in a Ranges down to a single value |
-- T --
| tile_ranges | Slide or tile over a Ranges object |
-- U --
| unanchor | Anchored Ranges objects |
| ungroup.GroupedGenomicRanges | Group a Ranges by one or more variables |
| union_ranges | Vector-wise Range set-operations |
| union_ranges_directed | Vector-wise Range set-operations |
-- W --
| write_bed | Write a BED or BEDGraph file |
| write_bed_graph | Write a BED or BEDGraph file |
| write_bigwig | Write a BigWig file |
| write_gff | Write a GFF(123) file |
| write_gff1 | Write a GFF(123) file |
| write_gff2 | Write a GFF(123) file |
| write_gff3 | Write a GFF(123) file |
| write_narrowpeaks | Write a BED or BEDGraph file |
| write_wig | Write a WIG file |
-- misc --
| %intersect% | Row-wise set operations on Ranges objects |
| %setdiff% | Row-wise set operations on Ranges objects |
| %union% | Row-wise set operations on Ranges objects |