Description Constructor Coercion Author(s) Examples
A BigWigSelection
represents a query against a
BigWig file, see import.bw
. It is simply
a RangedSelection that requires its colnames
parameter to be "score", if non-empty, as that is the only column
supported by BigWig.
BigWigSelection(ranges = GRanges(), colnames =
"score")
: Constructs a BigWigSelection
with the given
ranges
and colnames
. ranges
can be either
something coercible to a IntegerRangesList
,
a character
identifying a genome (see
GenomicSelection
), or a
BigWigFile
, in which case the ranges are
derived from the bounds of its sequences.
as(from, "BigWigSelection")
: Coerces from
to a
BigWigSelection
object. Typically, from
is a
GRanges
or
a IntegerRangesList
, the ranges of
which become the ranges in the
new BigWigSelection
.
Michael Lawrence
1 2 3 4 5 6 7 | rl <- IRangesList(chr1 = IRanges::IRanges(c(1, 5), c(3, 6)))
BigWigSelection(rl)
as(rl, "BigWigSelection") # same as above
# do not select the 'score' column
BigWigSelection(rl, character())
|
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
An object of class "BigWigSelection"
Slot "ranges":
IRangesList of length 1
$chr1
IRanges object with 2 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 1 3 3
[2] 5 6 2
Slot "colnames":
[1] "score"
An object of class "BigWigSelection"
Slot "ranges":
IRangesList of length 1
$chr1
IRanges object with 2 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 1 3 3
[2] 5 6 2
Slot "colnames":
[1] "score"
An object of class "BigWigSelection"
Slot "ranges":
IRangesList of length 1
$chr1
IRanges object with 2 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 1 3 3
[2] 5 6 2
Slot "colnames":
character(0)
Warning message:
system call failed: Cannot allocate memory
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