A fluent interface for manipulating GenomicRanges

Global functions | |
---|---|

BamFileOperator-class | Man page |

DeferredGenomicRanges-class | Man page |

FileOperator-class | Man page |

GroupedGenomicRanges-class | Man page |

GroupedIntegerRanges-class | Man page |

UQ | Man page |

UQS | Man page |

\%>\% | Man page |

\%intersect\% | Man page |

\%setdiff\% | Man page |

\%union\% | Man page |

add_na_seqlevels | Source code |

anchor | Man page Source code |

anchor.AnchoredGenomicRanges | Source code |

anchor_3p | Man page Source code |

anchor_3p.GenomicRanges | Source code |

anchor_5p | Man page Source code |

anchor_5p.GenomicRanges | Source code |

anchor_center | Man page Source code |

anchor_center.GenomicRanges | Source code |

anchor_center.IntegerRanges | Source code |

anchor_centre | Man page Source code |

anchor_end | Man page Source code |

anchor_end.GenomicRanges | Source code |

anchor_end.IntegerRanges | Source code |

anchor_start | Man page Source code |

anchor_start.GenomicRanges | Source code |

anchor_start.IntegerRanges | Source code |

are_bioc_pkgs_scoped | Source code |

arrange | Man page |

arrange.DelegatingGenomicRanges | Source code |

arrange.Ranges | Man page Source code |

as_granges | Man page Source code |

as_granges.data.frame | Source code |

as_granges.default | Source code |

as_iranges | Man page Source code |

as_iranges.data.frame | Source code |

as_iranges.default | Source code |

as_ranges | Man page Source code |

as_ranges.Rle | Source code |

as_ranges.RleList | Source code |

between | Man page Source code |

bind_ranges | Man page Source code |

bioc_generics | Source code |

check_names | Source code |

check_which_label | Source code |

chop_by_gaps | Man page Source code |

chop_by_gaps.DeferredGenomicRanges | Source code |

chop_by_gaps.GenomicRanges | Source code |

chop_by_introns | Man page Source code |

chop_by_introns.DeferredGenomicRanges | Source code |

chop_by_introns.GenomicRanges | Source code |

complement_ranges | Man page Source code |

complement_ranges.GenomicRanges | Source code |

complement_ranges.IntegerRanges | Source code |

complement_ranges_directed | Man page Source code |

complement_ranges_directed.GenomicRanges | Source code |

compute_coverage | Man page Source code |

compute_coverage.default | Source code |

count_overlaps | Man page Source code |

count_overlaps.GenomicRanges | Man page Source code |

count_overlaps.IntegerRanges | Man page Source code |

count_overlaps_directed | Man page Source code |

count_overlaps_directed.GenomicRanges | Man page Source code |

count_overlaps_within | Man page Source code |

count_overlaps_within.GenomicRanges | Man page Source code |

count_overlaps_within.IntegerRanges | Man page Source code |

count_overlaps_within_directed | Man page Source code |

count_overlaps_within_directed.GenomicRanges | Man page Source code |

detach_depends | Source code |

disjoin_ranges | Man page Source code |

disjoin_ranges.GenomicRanges | Source code |

disjoin_ranges.GroupedGenomicRanges | Source code |

disjoin_ranges.GroupedIntegerRanges | Source code |

disjoin_ranges.IntegerRanges | Source code |

disjoin_ranges_directed | Man page Source code |

disjoin_ranges_directed.GenomicRanges | Source code |

disjoin_ranges_directed.GroupedGenomicRanges | Source code |

enquo | Man page |

expand_by_hits | Source code |

expand_rng_by_cigar | Source code |

filter | Man page |

filter-ranges | Man page |

filter.BamFileOperator | Source code |

filter.DeferredGenomicRanges | Source code |

filter.DelegatingGenomicRanges | Source code |

filter.GroupedGenomicRanges | Source code |

filter.Ranges | Man page Source code |

filter_by_non_overlaps | Man page Source code |

filter_by_non_overlaps.GenomicRanges | Source code |

filter_by_non_overlaps.IntegerRanges | Source code |

filter_by_overlaps | Man page Source code |

filter_by_overlaps.BamFileOperator | Source code |

filter_by_overlaps.DeferredGenomicRanges | Source code |

filter_by_overlaps.GenomicRanges | Source code |

filter_by_overlaps.IntegerRanges | Source code |

filter_grp | Source code |

filter_rng | Source code |

find_overlaps | Man page Source code Source code |

find_overlaps.GenomicRanges | Man page Source code |

find_overlaps.IntegerRanges | Man page Source code |

find_overlaps_directed | Man page Source code |

find_overlaps_directed.GenomicRanges | Man page Source code |

find_overlaps_within | Man page Source code |

find_overlaps_within.GenomicRanges | Man page Source code |

find_overlaps_within.IntegerRanges | Man page Source code |

find_overlaps_within_directed | Man page Source code |

find_overlaps_within_directed.GenomicRanges | Man page Source code |

flank_downstream | Man page Source code |

flank_left | Man page Source code |

flank_right | Man page Source code |

flank_upstream | Man page Source code |

galn_to_grng | Source code |

genome_info | Man page Source code |

get_genome_info | Man page Source code |

get_genome_info.BamFileOperator | Source code |

get_genome_info.DeferredGenomicRanges | Source code |

get_genome_info.Seqinfo | Source code |

get_genome_info.default | Source code |

grng_construct | Source code |

group_by | Man page |

group_by-ranges | Man page |

group_by.DeferredGenomicRanges | Source code |

group_by.GenomicRanges | Man page Source code |

group_by.IntegerRanges | Source code |

group_by_overlaps | Man page Source code |

group_by_overlaps.GenomicRanges | Man page Source code |

group_by_overlaps.IntegerRanges | Man page Source code |

group_vars | Man page |

group_vars.GroupedGenomicRanges | Source code |

groups | Man page |

groups.GroupedGenomicRanges | Man page Source code |

groups.GroupedIntegerRanges | Man page |

initialize_AnchoredRanges | Source code |

initialize_GroupedRanges | Source code |

intersect_ranges | Man page Source code |

intersect_ranges.GenomicRanges | Source code |

intersect_ranges.IntegerRanges | Source code |

intersect_ranges_directed | Man page Source code |

intersect_ranges_directed.GenomicRanges | Source code |

interweave | Man page Source code |

irng_construct | Source code |

is_empty_delegate | Source code |

is_empty_quos | Source code |

join_follow | Man page Source code |

join_follow.GenomicRanges | Source code |

join_follow.IntegerRanges | Source code |

join_follow_left | Man page Source code |

join_follow_left.GenomicRanges | Source code |

join_follow_left.IntegerRanges | Source code |

join_follow_upstream | Man page Source code |

join_follow_upstream.GenomicRanges | Source code |

join_intersect | Source code |

join_nearest | Man page Source code |

join_nearest.GenomicRanges | Source code |

join_nearest.IntegerRanges | Source code |

join_nearest_downstream | Man page Source code |

join_nearest_downstream.GenomicRanges | Source code |

join_nearest_left | Man page Source code |

join_nearest_left.GenomicRanges | Source code |

join_nearest_left.IntegerRanges | Source code |

join_nearest_right | Man page Source code |

join_nearest_right.GenomicRanges | Source code |

join_nearest_right.IntegerRanges | Source code |

join_nearest_upstream | Man page Source code |

join_nearest_upstream.GenomicRanges | Source code |

join_overlap_inner | Man page Source code |

join_overlap_inner_directed | Man page Source code |

join_overlap_inner_within | Man page Source code |

join_overlap_inner_within_directed | Man page Source code |

join_overlap_intersect | Man page Source code |

join_overlap_intersect.GenomicRanges | Source code |

join_overlap_intersect.IntegerRanges | Source code |

join_overlap_intersect_directed | Man page Source code |

join_overlap_intersect_directed.GenomicRanges | Source code |

join_overlap_intersect_within | Man page Source code |

join_overlap_intersect_within.GenomicRanges | Source code |

join_overlap_intersect_within.IntegerRanges | Source code |

join_overlap_intersect_within_directed | Man page Source code |

join_overlap_intersect_within_directed.GenomicRanges | Source code |

join_overlap_left | Man page Source code Source code |

join_overlap_left.GenomicRanges | Source code |

join_overlap_left.IntegerRanges | Source code |

join_overlap_left_directed | Man page Source code |

join_overlap_left_directed.GenomicRanges | Source code |

join_overlap_left_within | Man page Source code |

join_overlap_left_within.GenomicRanges | Source code |

join_overlap_left_within.IntegerRanges | Source code |

join_overlap_left_within_directed | Man page Source code |

join_overlap_left_within_directed.GenomicRanges | Source code |

join_overlap_self | Man page Source code |

join_overlap_self.GenomicRanges | Source code |

join_overlap_self_directed | Man page Source code |

join_overlap_self_directed.GenomicRanges | Source code |

join_overlap_self_within | Man page Source code |

join_overlap_self_within.GenomicRanges | Source code |

join_overlap_self_within_directed | Man page Source code |

join_overlap_self_within_directed.GenomicRanges | Source code |

join_precede | Man page Source code |

join_precede.GenomicRanges | Source code |

join_precede.IntegerRanges | Source code |

join_precede_downstream | Man page Source code |

join_precede_downstream.GenomicRanges | Source code |

join_precede_right | Man page Source code |

join_precede_right.GenomicRanges | Source code |

join_precede_right.IntegerRanges | Source code |

load_delegate | Source code |

load_genomic_file | Source code |

load_genomic_file.BamFileOperator | Source code |

make_group_inx | Source code |

make_hits | Source code |

make_mcols | Source code |

mcols_overlaps_update | Source code |

mutate | Man page |

mutate.DeferredGenomicRanges | Source code |

mutate.DelegatingGenomicRanges | Source code |

mutate.GroupedGenomicRanges | Source code |

mutate.Ranges | Man page Source code |

mutate_core | Source code |

mutate_grp | Source code |

mutate_mcols | Source code |

mutate_rng | Source code |

n | Man page Source code |

na_cols | Source code |

na_ranges | Source code |

new_DeferredGenomicRanges | Source code |

new_anchored_gr | Source code |

new_anchored_ir | Source code |

new_bam_ops | Source code |

new_grouped_gr | Source code |

new_grouped_ir | Source code |

norm_args_reader | Source code |

norm_args_reader_gff | Source code |

overscope_eval_update | Source code |

overscope_ranges | Man page Source code |

overscope_ranges.DelegatingGenomicRanges | Source code |

overscope_ranges.GroupedGenomicRanges | Source code |

overscope_ranges.Ranges | Source code |

pair_follow | Man page Source code |

pair_follow.GenomicRanges | Source code |

pair_follow.IntegerRanges | Source code |

pair_nearest | Man page Source code |

pair_nearest.GenomicRanges | Source code |

pair_nearest.IntegerRanges | Source code |

pair_overlaps | Man page Source code |

pair_overlaps.GenomicRanges | Source code |

pair_overlaps.IntegerRanges | Source code |

pair_precede | Man page Source code |

pair_precede.GenomicRanges | Source code |

pair_precede.IntegerRanges | Source code |

paired_alignments | Source code |

partition_rng | Source code |

plyranges | Man page |

plyranges-package | Man page |

quos | Man page |

ranges-info | Man page |

ranges_vars | Source code |

read_bam | Man page Source code |

read_bed | Man page Source code |

read_bed_graph | Man page Source code |

read_bigwig | Man page Source code |

read_gff | Man page Source code |

read_gff1 | Man page Source code |

read_gff2 | Man page Source code |

read_gff3 | Man page Source code |

read_narrowpeaks | Man page Source code |

read_wig | Man page Source code |

reattach_depends | Source code |

reduce_by_grp | Source code |

reduce_ranges | Man page Source code |

reduce_ranges.GenomicRanges | Source code |

reduce_ranges.GroupedGenomicRanges | Source code |

reduce_ranges.GroupedIntegerRanges | Source code |

reduce_ranges.IntegerRanges | Source code |

reduce_ranges_directed | Man page Source code |

reduce_ranges_directed.GenomicRanges | Source code |

reduce_ranges_directed.GroupedGenomicRanges | Source code |

reduce_rng | Source code |

reduce_single | Source code |

reexports | Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page |

rename_dots | Source code |

resize_by_strand | Source code |

rng_arrange | Source code |

scope_plyranges | Source code |

select | Man page |

select.BamFileOperator | Source code |

select.DeferredGenomicRanges | Source code |

select.DelegatingGenomicRanges | Source code |

select.Ranges | Man page Source code |

select_rng | Source code |

set_end | Man page Source code |

set_end.Ranges | Source code |

set_genome_info | Man page Source code |

set_seqnames | Man page Source code |

set_seqnames.GenomicRanges | Source code |

set_start | Man page Source code |

set_start.Ranges | Source code |

set_strand | Man page Source code |

set_strand.GenomicRanges | Source code |

set_width | Man page Source code |

set_width.AnchoredGenomicRanges | Source code |

set_width.AnchoredIntegerRanges | Source code |

set_width.Ranges | Source code |

setdiff_ranges | Man page Source code |

setdiff_ranges.GenomicRanges | Source code |

setdiff_ranges.IntegerRanges | Source code |

setdiff_ranges_directed | Man page Source code |

setdiff_ranges_directed.GenomicRanges | Source code |

shift_downstream | Man page Source code |

shift_left | Man page Source code |

shift_right | Man page Source code |

shift_upstream | Man page Source code |

show_AnchoredRanges | Source code |

show_GroupedRanges | Source code |

slide_ranges | Man page Source code |

slide_ranges.Ranges | Source code |

span | Man page Source code |

stretch | Man page Source code |

stretch.AnchoredGenomicRanges | Source code |

stretch.AnchoredIntegerRanges | Source code |

stretch.Ranges | Source code |

stretch_by_strand | Source code |

stretch_center | Source code |

summarise | Man page |

summarise.DeferredGenomicRanges | Source code |

summarise.DelegatingGenomicRanges | Source code |

summarise.DelegatingIntegerRanges | Source code |

summarise.GroupedGenomicRanges | Source code |

summarise.Ranges | Man page Source code |

summarize | Man page |

summarize_rng | Source code |

tbl_vars.GenomicRanges | Source code |

tile_ranges | Man page Source code |

tile_ranges.Ranges | Source code |

unanchor | Man page Source code |

unanchor.AnchoredGenomicRanges | Source code |

ungroup | Man page |

ungroup.GroupedGenomicRanges | Man page Source code |

union_ranges | Man page Source code |

union_ranges.GenomicRanges | Source code |

union_ranges.IntegerRanges | Source code |

union_ranges_directed | Man page Source code |

union_ranges_directed.GenomicRanges | Source code |

unnest | Man page |

unnest.GenomicRanges | Man page Source code |

unpaired_alignments | Source code |

validAnchoredRanges | Source code |

validGroupedRanges | Source code |

valid_flag_filters | Source code |

write_bed | Man page Source code |

write_bed_graph | Man page Source code |

write_bigwig | Man page Source code |

write_gff | Man page Source code |

write_gff1 | Man page Source code |

write_gff2 | Man page Source code |

write_gff3 | Man page Source code |

write_narrowpeaks | Man page Source code |

write_wig | Man page Source code |

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