API for LiNk-NY/GenomicRanges
Representation and manipulation of genomic intervals and variables defined along a genome

Global functions
$,GenomicRanges-method Man page
$<-,GenomicRanges-method Man page
Constraint Man page
Constraint-class Man page
ConstraintORNULL Man page
ConstraintORNULL-class Man page
Constraints Man page
DelegatingGenomicRanges-class Man page Man page
DollarNames.GenomicRanges Source code
GNCList Man page Source code
GNCList-class Man page
GPos Man page Source code
GPos-class Man page
GRanges Man page Man page Source code
GRanges-class Man page
GRangesList Man page Man page Source code
GRangesList-class Man page
GenomicRanges Man page
GenomicRanges-class Man page
GenomicRanges-comparison Man page
GenomicRangesList Man page Source code
GenomicRangesList-class Man page
GenomicRangesORGRangesList-class Man page
GenomicRangesORmissing-class Man page
GenomicRanges_as_IntegerQuads Source code
GenomicRanges_findNearest0 Source code
GenomicRanges_findPrecedeFollow Source code
GenomicRanges_summary Source code
Hits Source code
Ops,GenomicRanges,numeric-method Man page
SimpleGenomicRangesList-class Man page
[,GRangesList,ANY-method Man page
[,GenomicRanges,ANY-method Man page
[,List,GenomicRanges-method Man page
[,list,GenomicRanges-method Man page
[<-,GRanges-method Man page
[<-,GRangesList,ANY,ANY,ANY-method Man page
[<-,GRangesList,ANY-method Man page
[<-,GRangesList-method Man page
[<-,GenomicRanges,ANY,ANY,ANY-method Man page
[[<-,GRangesList,ANY,ANY-method Man page
[[<-,GRangesList,ANY-method Man page
[[<-,GRangesList-method Man page
absoluteRanges Man page Source code
aggregated_sum Source code
allCompatibleSeqnamesAndStrand Source code
as.character,GenomicRanges-method Man page
as.data.frame,GPos-method Man page
as.data.frame,GenomicRanges-method Man page
as.factor,GenomicRanges-method Man page
bindAsGRanges Man page Source code
binnedAverage Man page Source code
c,GPos-method Man page
c,GenomicRanges-method Man page
checkConstraint Man page
checkParms Source code
class:Constraint Man page
class:ConstraintORNULL Man page
class:DelegatingGenomicRanges Man page Man page
class:GNCList Man page
class:GPos Man page
class:GRanges Man page
class:GRangesList Man page
class:GenomicRanges Man page
class:GenomicRangesList Man page
class:SimpleGenomicRangesList Man page
coerce,ANY,GenomicRanges-method Man page
coerce,DataFrame,GRanges-method Man page
coerce,GNCList,GRanges-method Man page
coerce,GRanges,GRangesList-method Man page
coerce,GRangesList,CompressedIRangesList-method Man page
coerce,GRangesList,IRangesList-method Man page
coerce,GRangesList,RangesList-method Man page
coerce,GenomicRanges,GNCList-method Man page
coerce,GenomicRanges,GPos-method Man page
coerce,GenomicRanges,GRanges-method Man page
coerce,GenomicRanges,Grouping-method Man page
coerce,GenomicRanges,RangedData-method Man page
coerce,GenomicRanges,RangesList-method Man page
coerce,RangedData,GRanges-method Man page
coerce,RangesList,GRanges-method Man page
coerce,RleList,GRanges-method Man page
coerce,RleViewsList,GRanges-method Man page
coerce,Seqinfo,GRanges-method Man page
coerce,Seqinfo,RangesList-method Man page
coerce,character,GRanges-method Man page
coerce,data.frame,GRanges-method Man page
coerce,factor,GRanges-method Man page
coerce,list,GRangesList-method Man page
collect_prefixes Source code
combine_GPos_objects Source code
compatibleSeqnames Source code
constraint Man page
constraint<- Man page
countOverlaps Man page
countOverlaps,GenomicRanges,GenomicRanges-method Man page
countOverlaps_GenomicRanges Source code
coverage Man page
coverage,GRangesList-method Man page
coverage,GenomicRanges-method Man page
coverage-methods Man page
dBracketReplaceGRList Source code
deconstructGRLintoGR Source code
deconstructGRintoRGL Source code
disjoin Man page
disjoin,GRangesList-method Man page
disjoin,GenomicRanges-method Man page
disjoin,GenomicRangesList-method Man page
disjointBins Man page
disjointBins,GenomicRanges-method Man page
distance Man page
distance,GenomicRanges,GenomicRanges-method Man page
distanceToNearest Man page Source code
distanceToNearest,GenomicRanges,GenomicRanges-method Man page
distanceToNearest,GenomicRanges,missing-method Man page
duplicated,GenomicRanges-method Man page
duplicated.GenomicRanges Man page Source code Source code
elementMetadata,GRangesList-method Man page
elementMetadata<-,GRangesList-method Man page
end,GNCList-method Man page
end,GPos-method Man page
end,GRangesList-method Man page
end,GenomicRanges-method Man page
end<-,GRangesList-method Man page
end<-,GenomicRanges-method Man page
extraColumnSlots Source code
extraColumnSlotsAsDF Source code
extractROWS,GPos-method Man page
extract_groups_from_GenomicRanges Source code
fast_binary_mendoapply Source code
filterHits Source code
findKNN Source code
findNearest_distance Source code
findOverlaps Man page
findOverlaps,GRangesList,GRangesList-method Man page
findOverlaps,GRangesList,GenomicRanges-method Man page
findOverlaps,GenomicRanges,GRangesList-method Man page
findOverlaps,GenomicRanges,GenomicRanges-method Man page
findOverlaps,RangedData,GenomicRanges-method Man page
findOverlaps-methods Man page
findOverlaps_GNCList Source code
findOverlaps_GenomicRanges Source code
findPrecedeFollow_pmin Source code
find_GRanges_cols Source code
find_seqnames_col Source code
find_start_end_cols Source code
find_strand_col Source code
find_width_col Source code
fix_inner_revmap_mcol Source code
flank Man page
flank,GRangesList-method Man page
flank,GenomicRanges-method Man page
flank,GenomicRangesList-method Man page
follow Man page
follow,GenomicRanges,GenomicRanges-method Man page
follow,GenomicRanges,missing-method Man page
from_GenomicRanges_to_GPos Source code
from_Seqinfo_to_GRanges Source code
from_character_to_GRanges Source code
from_factor_to_GRanges Source code
gaps Man page
gaps,GenomicRanges-method Man page
genomicvariables Man page
genomicvars Man page
get_GRangesList_mcols Source code
get_circle_length Source code
get_data_frame_col_as_numeric Source code
get_out_of_bound_index Source code
get_relative_ends Source code
get_relative_starts Source code
granges Man page
granges,GNCList-method Man page
granges,GenomicRanges-method Man page
grglist Man page
grglist,Pairs-method Man page
hasHead Source code
inter-range-methods Man page
intersect Man page
intersect,GRangesList,GRangesList-method Man page
intersect,GenomicRanges,GenomicRanges-method Man page
intersect,GenomicRanges,Vector-method Man page
intersect,Vector,GenomicRanges-method Man page
intra-range-methods Man page
invertStrand,NULL-method Man page
invertStrand,Rle-method Man page
invertStrand,RleList-method Man page
invertStrand,character-method Man page
invertStrand,factor-method Man page
invertStrand,integer-method Man page
invertStrand,logical-method Man page
is.unsorted,GenomicRanges-method Man page
isDisjoint Man page
isDisjoint,GPos-method Man page
isDisjoint,GRangesList-method Man page
isDisjoint,GenomicRanges-method Man page
isDisjoint,GenomicRangesList-method Man page
isSmallGenome Man page Source code
length,GNCList-method Man page
length,GPos-method Man page
length,GenomicRanges-method Man page
makeGRangesFromDataFrame Man page Source code
makeGRangesListFromDataFrame Man page Source code
makeGRangesListFromFeatureFragments Man page Source code
make_breakpoints_for_cut_last_tile_in_chrom Source code
make_naked_matrix_from_GPos Source code
make_naked_matrix_from_GenomicRanges Source code
make_out_of_bound_warning_msg Source code
make_spaceid Source code
match,GenomicRanges,GenomicRanges-method Man page
maxEndPerGRangesSequence Source code
mcolAsRleList Man page Source code
minStartPerGRangesSequence Source code
names,GNCList-method Man page
names,GPos-method Man page
names,GenomicRanges-method Man page
names<-,GPos-method Man page
names<-,GenomicRanges-method Man page
narrow Man page
narrow,GRangesList-method Man page
narrow,GenomicRanges-method Man page
narrow,GenomicRangesList-method Man page
nearest Man page Source code
nearest,GenomicRanges,GenomicRanges-method Man page
nearest,GenomicRanges,missing-method Man page
nearest-methods Man page
nearestDistance Source code
new_GRanges Source code
nextCheckConstraintSignatures Source code
normalize_seqnames_replacement_value Source code
normargGenomicRangesStrand Source code
normargListOfIntegers Source code
normarg_field Source code
normarg_seqinfo Source code
normarg_seqlengths Source code
normarg_shift_or_weight Source code
nvert_strand_factor Source code
onUnload Source code
order,GenomicRanges-method Man page
orderNumeric Source code
order_GenomicRanges Source code
overlap_score Source code
overlapsAny Man page
pcompare Man page
pcompare,GenomicRanges,GenomicRanges-method Man page
pcompare_GenomicRanges Source code
pgap Man page
pgap,GRanges,GRanges-method Man page
phicoef Man page Source code
pintersect Man page
pintersect,GRanges,GRanges-method Man page
pintersect,GRanges,GRangesList-method Man page
pintersect,GRangesList,GRanges-method Man page
pintersect_GRangesList_GRanges Source code
pintersect_GRanges_GRanges Source code
pos Man page
pos,GPos-method Man page
precede Man page
precede,GenomicRanges,GenomicRanges-method Man page
precede,GenomicRanges,missing-method Man page
promoters Man page
promoters,GRangesList-method Man page
promoters,GenomicRanges-method Man page
promoters,GenomicRangesList-method Man page
psetdiff Man page
psetdiff,GRanges,GRanges-method Man page
psetdiff,GRanges,GRangesList-method Man page
punion Man page
punion,GRanges,GRanges-method Man page
punion,GRanges,GRangesList-method Man page
punion,GRangesList,GRanges-method Man page
range Man page
range,GPos-method Man page
range,GRangesList-method Man page
range,GenomicRanges-method Man page
range,GenomicRangesList-method Man page
range-squeezers Man page
ranges,DelegatingGenomicRanges-method Man page
ranges,GNCList-method Man page
ranges,GPos-method Man page
ranges,GRanges-method Man page
ranges,GRangesList-method Man page
ranges<-,GRangesList-method Man page
ranges<-,GenomicRanges-method Man page
rank,GenomicRanges-method Man page
reconstructGRLfromGR Source code
reconstructGRfromRGL Source code
recycle Source code
reduce Man page
reduce,GRangesList-method Man page
reduce,GenomicRanges-method Man page
reduce,GenomicRangesList-method Man page
relativeRanges Man page Source code
relevelSeqnamesForMatch Source code
relistToClass,GRanges-method Man page
resize Man page
resize,GRangesList-method Man page
resize,GenomicRanges-method Man page
resize,GenomicRangesList-method Man page
restrict Man page
restrict,GRangesList-method Man page
restrict,GenomicRanges-method Man page
restrict,GenomicRangesList-method Man page
restrictRngs Source code
rglist Man page
rglist,Pairs-method Man page
sBracketReplaceGRList Source code
sBracketSubsetGRList Source code
score,GRangesList-method Man page
score,GenomicRanges-method Man page
score<-,GRangesList-method Man page
score<-,GenomicRanges-method Man page
selfmatch,GenomicRanges-method Man page
seqinfo,DelegatingGenomicRanges-method Man page
seqinfo,GNCList-method Man page
seqinfo,GPos-method Man page
seqinfo,GRanges-method Man page
seqinfo,GRangesList-method Man page
seqinfo,List-method Man page
seqinfo,RangedData-method Man page
seqinfo,RangesList-method Man page
seqinfo<-,GPos-method Man page
seqinfo<-,GRangesList-method Man page
seqinfo<-,GenomicRanges-method Man page
seqinfo<-,List-method Man page
seqinfo<-,RangedData-method Man page
seqnames,DelegatingGenomicRanges-method Man page
seqnames,GNCList-method Man page
seqnames,GPos-method Man page
seqnames,GRanges-method Man page
seqnames,GRangesList-method Man page
seqnames,RangedData-method Man page
seqnames<-,GRangesList-method Man page
seqnames<-,GenomicRanges-method Man page
set_GRangesList_mcols Source code
set_GRangesList_seqinfo Source code
set_GRangesList_seqnames Source code
set_GRangesList_strand Source code
set_GenomicRanges_seqinfo Source code
set_strand_mcols_seqinfo Source code
setdiff Man page
setdiff,GRangesList,GRangesList-method Man page
setdiff,GenomicRanges,GenomicRanges-method Man page
setdiff,GenomicRanges,Vector-method Man page
setdiff,Vector,GenomicRanges-method Man page
setops-methods Man page
shift Man page
shift,GPos-method Man page
shift,GRangesList-method Man page
shift,GenomicRanges-method Man page
shift,GenomicRangesList-method Man page
show,GPos-method Man page
show,GRangesList-method Man page
show,GenomicRanges-method Man page
showList Source code
show_GPos Source code
show_GenomicRanges Source code
slidingWindows Man page
slidingWindows,GenomicRanges-method Man page
sort,GenomicRanges-method Man page
sort.GenomicRanges Man page Source code Source code
start,GNCList-method Man page
start,GPos-method Man page
start,GRangesList-method Man page
start,GenomicRanges-method Man page
start<-,GRangesList-method Man page
start<-,GenomicRanges-method Man page
stitch_GenomicRanges Source code
strand,DataTable-method Man page
strand,DelegatingGenomicRanges-method Man page
strand,GNCList-method Man page
strand,GPos-method Man page
strand,GRanges-method Man page
strand,GRangesList-method Man page
strand,NULL-method Man page
strand,Rle-method Man page
strand,RleList-method Man page
strand,character-method Man page
strand,factor-method Man page
strand,integer-method Man page
strand,logical-method Man page
strand,missing-method Man page
strand-utils Man page
strand<-,DataTable,ANY-method Man page
strand<-,GRangesList,ANY-method Man page
strand<-,GRangesList,character-method Man page
strand<-,GenomicRanges,ANY-method Man page
subsetByOverlaps Man page
subset_by_GenomicRanges Source code
summary,GenomicRanges-method Man page
summary.GenomicRanges Man page Source code
superimpose_breakpoints Source code
test Source code
tile Man page
tile,GenomicRanges-method Man page
tile-methods Man page
tileGenome Man page Source code
translate_revmap Source code
trim,GenomicRanges-method Man page
union Man page
union,GRangesList,GRangesList-method Man page
union,GenomicRanges,GenomicRanges-method Man page
union,GenomicRanges,Vector-method Man page
union,Vector,GenomicRanges-method Man page
unlist_list_of_GenomicRanges Source code
unsafe.transcriptLocs2refLocs Source code
unsafe.transcriptWidths Source code
unsupported_intersect Source code
unsupported_setdiff Source code
unsupported_union Source code
updateObject,GRanges-method Man page
updateObject,GRangesList-method Man page
valid.GRanges Source code
valid.GRanges.mcols Source code
valid.GRanges.ranges Source code
valid.GRangesList Source code
valid.GRangesList.mcols Source code
valid.GenomicRanges Source code
valid.GenomicRanges.ecs Source code
valid.GenomicRanges.length Source code
valid.GenomicRanges.mcols Source code
valid.GenomicRanges.ranges Source code
valid.GenomicRanges.seqinfo Source code
valid.GenomicRanges.seqnames Source code
valid.GenomicRanges.strand Source code
width,GNCList-method Man page
width,GPos-method Man page
width,GRangesList-method Man page
width,GenomicRanges-method Man page
width<-,GRangesList-method Man page
width<-,GenomicRanges-method Man page
window,GenomicRanges-method Man page
LiNk-NY/GenomicRanges documentation built on May 9, 2017, 5:14 a.m.