API for plyranges
A fluent interface for manipulating GenomicRanges

Global functions
!! Man page
!!! Man page
%>% Man page
%intersect% Man page
%setdiff% Man page
%union% Man page
BamFileOperator-class Man page
DeferredGenomicRanges-class Man page
FileOperator-class Man page
GroupedGenomicRanges-class Man page
GroupedIntegerRanges-class Man page
add_na_seqlevels Source code
all_genomic_ranges Source code
all_integer_ranges 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
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
bind_rng Source code
bioc_generics Source code
check_id_var 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
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
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
group_vars.Ranges Source code
groups Man page
groups.GroupedGenomicRanges Man page Source code
groups.GroupedIntegerRanges Man page
groups.Ranges Source code
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
n_distinct 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
quo_set_generic Source code
quos_set_env Source code
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
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
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_dots_named Source code
set_dots_unnamed Source code
set_end Man page Source code
set_end.Ranges Source code
set_genome_info Man page Source code
set_id_var 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
tidyverse-reexports Man page
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
ungroup.Ranges 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
plyranges documentation built on Nov. 1, 2018, 3:58 a.m.