API for Bioconductor-mirror/InteractionSet
Base Classes for Storing Genomic Interaction Data

Global functions
$,GInteractions-method Man page
$<-,GInteractions-method Man page
ContactMatrix Man page
ContactMatrix,ANY,GRanges,GRanges,GenomicRanges_OR_missing-metho Man page
ContactMatrix,ANY,numeric,numeric,GRanges-method Man page
ContactMatrix,missing,missing,missing,GenomicRanges_OR_missing-m Man page
ContactMatrix-access Man page
ContactMatrix-class Man page
ContactMatrix-dist Man page
ContactMatrix-sort Man page
ContactMatrix-subset Man page
GInteractions Man page
GInteractions,GRanges,GRanges,GenomicRanges_OR_missing-method Man page
GInteractions,missing,missing,GenomicRanges_OR_missing-method Man page
GInteractions,numeric,numeric,GRanges-method Man page
GInteractions-class Man page
ISetToRSE Source code
Interaction-overlaps Man page
InteractionSet Man page
InteractionSet,ANY,GInteractions-method Man page
InteractionSet,missing,missing-method Man page
InteractionSet-class Man page
ReverseStrictGInteractions-class Man page
StrictGInteractions-class Man page
[,ContactMatrix,ANY,ANY,ANY-method Man page
[,ContactMatrix,ANY,ANY-method Man page
[,ContactMatrix,ANY-method Man page
[,InteractionSet,ANY,ANY,ANY-method Man page
[,InteractionSet,ANY,ANY-method Man page
[,InteractionSet,ANY-method Man page
[<-,ContactMatrix,ANY,ANY,ContactMatrix-method Man page
[<-,GInteractions,ANY,GInteractions-method Man page
[<-,InteractionSet,ANY,ANY,InteractionSet-method Man page
anchor.fun.gen Source code
anchor.repfun.gen Source code
anchorIds<- Man page
anchorIds<-,ContactMatrix-method Man page
anchorIds<-,GInteractions-method Man page
anchorIds<-,InteractionSet-method Man page
anchorIds<-,ReverseStrictGInteractions-method Man page
anchorIds<-,StrictGInteractions-method Man page
anchors Man page
anchors,ContactMatrix-method Man page
anchors,GInteractions-method Man page
anchors,InteractionSet-method Man page
anchors<- Man page
anchors<-,ContactMatrix-method Man page
anchors<-,GInteractions-method Man page
anchors<-,InteractionSet-method Man page
anchors<-,ReverseStrictGInteractions-method Man page
anchors<-,StrictGInteractions-method Man page
appendRegions<- Man page
appendRegions<-,ContactMatrix-method Man page
appendRegions<-,GInteractions-method Man page
appendRegions<-,InteractionSet-method Man page
as.data.frame,GInteractions-method Man page
as.matrix,ContactMatrix-method Man page
as.matrix<- Man page
as.matrix<-,ContactMatrix-method Man page
boundingBox Man page Source code
boundingBox,GInteractions-method Man page
boundingBox,InteractionSet-method Man page
c,GInteractions-method Man page
cbind,ContactMatrix-method Man page
cbind,InteractionSet-method Man page
check_inputs Source code
chooseRegion Source code
coerce_to_union Source code
collate_GRanges Source code
countOverlaps Man page
countOverlaps,GInteractions,GInteractions-method Man page
countOverlaps,GInteractions,InteractionSet-method Man page
countOverlaps,GInteractions,Vector-method Man page
countOverlaps,GInteractions,missing-method Man page
countOverlaps,InteractionSet,GInteractions-method Man page
countOverlaps,InteractionSet,InteractionSet-method Man page
countOverlaps,InteractionSet,Vector-method Man page
countOverlaps,InteractionSet,missing-method Man page
countOverlaps,Vector,GInteractions-method Man page
countOverlaps,Vector,InteractionSet-method Man page
decode_region_mode Source code
deflate Man page
deflate,ContactMatrix-method Man page
dim,ContactMatrix-method Man page
dimnames,ContactMatrix-method Man page
dimnames<-,ContactMatrix,ANY-method Man page
dimnames<-,ContactMatrix-method Man page
duplicated,ContactMatrix-method Man page
duplicated,GInteractions-method Man page
duplicated,InteractionSet-method Man page
enforce_order Source code
fast_overlap Source code
findOverlaps Man page
findOverlaps,GInteractions,GInteractions-method Man page
findOverlaps,GInteractions,InteractionSet-method Man page
findOverlaps,GInteractions,Vector-method Man page
findOverlaps,GInteractions,missing-method Man page
findOverlaps,InteractionSet,GInteractions-method Man page
findOverlaps,InteractionSet,InteractionSet-method Man page
findOverlaps,InteractionSet,Vector-method Man page
findOverlaps,InteractionSet,missing-method Man page
findOverlaps,Vector,GInteractions-method Man page
findOverlaps,Vector,InteractionSet-method Man page
first Man page
first,GInteractions-method Man page
first,InteractionSet-method Man page
flipGI Source code
get_dist_output Source code
get_olap_bounds Source code
get_used Source code
inflate Man page
inflate,GInteractions-method Man page
inflate,InteractionSet-method Man page
interaction-access Man page
interaction-bind Man page
interaction-compare Man page
interaction-subset Man page
interactions Man page
interactions,InteractionSet-method Man page
interactions<- Man page
interactions<-,InteractionSet-method Man page
intrachr Man page
intrachr,ContactMatrix-method Man page
intrachr,GInteractions-method Man page
intrachr,InteractionSet-method Man page
length,ContactMatrix-method Man page
length,GInteractions-method Man page
linear_olap_finder Source code
linearize Man page Source code
linearize,GInteractions,GRanges-method Man page
linearize,GInteractions,numeric-method Man page
linearize,InteractionSet,GRanges-method Man page
linearize,InteractionSet,numeric-method Man page
linkOverlap Source code
linkOverlaps Man page
linkOverlaps,GInteractions,GRanges,GRanges-method Man page
linkOverlaps,GInteractions,GRanges,missing-method Man page
linkOverlaps,InteractionSet,GRanges,GRanges-method Man page
linkOverlaps,InteractionSet,GRanges,missing-method Man page
makeGInteractionsFromGRangesPairs Man page Source code
makeNakedMatFromGInteractions Source code
make_to_indices Source code
match,GInteractions,GInteractions-method Man page
match,GInteractions,InteractionSet-method Man page
match,InteractionSet,GInteractions-method Man page
match,InteractionSet,InteractionSet-method Man page
mcols,InteractionSet-method Man page
mcols<-,InteractionSet-method Man page
names,GInteractions-method Man page
names,InteractionSet-method Man page
names<-,GInteractions-method Man page
names<-,InteractionSet-method Man page
new_ContactMatrix Source code
new_GInteractions Source code
new_InteractionSet Source code
olap.fun.gen Source code
order,ContactMatrix-method Man page
order,GInteractions-method Man page
order,InteractionSet-method Man page
overlapsAny Man page
overlapsAny,ContactMatrix,GInteractions-method Man page
overlapsAny,ContactMatrix,GRanges-method Man page
overlapsAny,ContactMatrix,GRangesList-method Man page
overlapsAny,ContactMatrix,InteractionSet-method Man page
overlapsAny,GInteractions,GInteractions-method Man page
overlapsAny,GInteractions,InteractionSet-method Man page
overlapsAny,GInteractions,Vector-method Man page
overlapsAny,GInteractions,missing-method Man page
overlapsAny,InteractionSet,GInteractions-method Man page
overlapsAny,InteractionSet,InteractionSet-method Man page
overlapsAny,InteractionSet,Vector-method Man page
overlapsAny,InteractionSet,missing-method Man page
overlapsAny,Vector,GInteractions-method Man page
overlapsAny,Vector,InteractionSet-method Man page
pairdist Man page
pairdist,ContactMatrix-method Man page
pairdist,GInteractions-method Man page
pairdist,InteractionSet-method Man page
paired_overlap_finder2 Source code
pairs Man page
pairs,GInteractions-method Man page
pairs,InteractionSet-method Man page
pasteAnchor Source code
pcompare,GInteractions,GInteractions-method Man page
rbind,ContactMatrix-method Man page
rbind,InteractionSet-method Man page
reduceRegions Man page
reduceRegions,ContactMatrix-method Man page
reduceRegions,GInteractions-method Man page
reduceRegions,InteractionSet-method Man page
regions Man page
regions,ContactMatrix-method Man page
regions,GInteractions-method Man page
regions,InteractionSet-method Man page
regions<- Man page
regions<-,ContactMatrix-method Man page
regions<-,GInteractions-method Man page
regions<-,InteractionSet-method Man page
replaceRegions<- Man page
replaceRegions<-,ContactMatrix-method Man page
replaceRegions<-,GInteractions-method Man page
replaceRegions<-,InteractionSet-method Man page
resort_regions Source code
safeNMcols Source code
scat Source code
second Man page
second,GInteractions-method Man page
second,InteractionSet-method Man page
seqinfo,GInteractions-method Man page
seqinfo,InteractionSet-method Man page
seqinfo<-,GInteractions-method Man page
seqinfo<-,InteractionSet-method Man page
show,ContactMatrix-method Man page
show,GInteractions-method Man page
show,InteractionSet-method Man page
showGInteractions Source code
sort,ContactMatrix-method Man page
sort,GInteractions-method Man page
sort,InteractionSet-method Man page
strict_check Source code
subset,ContactMatrix-method Man page
subset,InteractionSet-method Man page
subsetByOverlaps Man page
subsetByOverlaps,GInteractions,GInteractions-method Man page
subsetByOverlaps,GInteractions,InteractionSet-method Man page
subsetByOverlaps,GInteractions,Vector-method Man page
subsetByOverlaps,InteractionSet,GInteractions-method Man page
subsetByOverlaps,InteractionSet,InteractionSet-method Man page
subsetByOverlaps,InteractionSet,Vector-method Man page
subsetByOverlaps,Vector,GInteractions-method Man page
subsetByOverlaps,Vector,InteractionSet-method Man page
swapAnchors Man page
swapAnchors,GInteractions-method Man page
swapAnchors,InteractionSet-method Man page
t,ContactMatrix-method Man page
trim,ContactMatrix-method Man page
trim,GInteractions-method Man page
trim,InteractionSet-method Man page
unflipGI Source code
unique,ContactMatrix-method Man page
unique,GInteractions-method Man page
unique,InteractionSet-method Man page
width,ContactMatrix-method Man page
width,GInteractions-method Man page
width,InteractionSet-method Man page
Bioconductor-mirror/InteractionSet documentation built on June 23, 2017, 3:14 p.m.