API for plyranges
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
plyranges documentation built on June 7, 2018, 6:01 p.m.