/usr/lib/R/site-library/GenomicRanges/NAMESPACE is in r-bioc-genomicranges 1.30.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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import(methods)
importFrom(utils, as.roman, .DollarNames)
importFrom(stats, setNames)
importFrom(stats4, summary)
import(BiocGenerics)
import(S4Vectors)
import(IRanges)
import(GenomeInfoDb)
import(XVector) # only for the "Views" method for integer vectors, the
# XIntegerViews class, and the "viewMins", "viewMaxs", and
# "viewSums" methods for XIntegerViews objects
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 classes
###
exportClasses(
Constraint, Constraint_OR_NULL,
GenomicRanges, GenomicRanges_OR_missing,
IRanges_OR_IPos, GRanges, GPos,
DelegatingGenomicRanges,
GNCList,
GRangesList, GenomicRanges_OR_GRangesList,
GenomicRangesList, SimpleGenomicRangesList
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S3 methods
###
S3method(.DollarNames, GenomicRanges)
S3method(.DollarNames, GRanges)
S3method(duplicated, GenomicRanges)
S3method(sort, GenomicRanges)
S3method(summary, GenomicRanges)
### We also export them thru the export() directive so that (a) they can be
### called directly, (b) tab-completion on the name of the generic shows them,
### and (c) methods() doesn't asterisk them.
export(
duplicated.GenomicRanges,
sort.GenomicRanges,
summary.GenomicRanges
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 methods for generics not defined in GenomicRanges
###
exportMethods(
length,
names, "names<-",
"[", "[<-", "[[", "[[<-", "$", "$<-",
as.character, as.factor, as.data.frame,
coerce,
c,
show,
split, unlist,
range,
Ops,
merge,
## Generics defined in the stats4 package:
summary,
## Generics defined in the BiocGenerics package:
duplicated, match,
is.unsorted, order, sort, rank,
union, intersect, setdiff,
start, "start<-", end, "end<-", width, "width<-",
strand, "strand<-", invertStrand,
score, "score<-",
updateObject,
## Generics defined in S4Vectors:
elementMetadata, "elementMetadata<-",
mcols, "mcols<-",
values, "values<-",
selfmatch,
relistToClass,
pcompare,
## Generics defined in IRanges:
ranges, "ranges<-",
rglist,
pos,
findOverlaps, countOverlaps,
shift, narrow, resize, flank, promoters, restrict, trim,
reduce, gaps, disjoin, isDisjoint, disjointBins,
coverage,
punion, pintersect, psetdiff, pgap,
precede, follow, nearest, distance, distanceToNearest,
tile, slidingWindows,
## Generics defined in GenomeInfoDb:
seqinfo, "seqinfo<-",
seqnames, "seqnames<-"
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export non-generic functions
###
export(
phicoef,
GRanges, .DollarNames.GenomicRanges, .DollarNames.GRanges,
GPos,
GNCList,
GenomicRangesList, GRangesList,
makeGRangesFromDataFrame,
makeGRangesListFromDataFrame,
makeGRangesListFromFeatureFragments,
isSmallGenome, absoluteRanges, relativeRanges,
tileGenome,
bindAsGRanges, mcolAsRleList, binnedAverage
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 generics defined in GenomicRanges + export corresponding
### methods
###
export(
## constraint.R:
#constraint, "constraint<-",
checkConstraint,
## genomic-range-squeezers.R:
granges, grglist
)
### Exactly the same list as above.
exportMethods(
#constraint, "constraint<-",
checkConstraint,
granges, grglist
)
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