Intra range transformations of a RangedSummarizedExperiment object

Description

This man page documents the intra range transformations that are supported on RangedSummarizedExperiment objects.

Usage

## S4 method for signature 'RangedSummarizedExperiment'
shift(x, shift=0L, use.names=TRUE)

## S4 method for signature 'RangedSummarizedExperiment'
narrow(x, start=NA, end=NA, width=NA, use.names=TRUE)

## S4 method for signature 'RangedSummarizedExperiment'
resize(x, width, fix="start", use.names=TRUE,
       ignore.strand=FALSE)

## S4 method for signature 'RangedSummarizedExperiment'
flank(x, width, start=TRUE, both=FALSE,
      use.names=TRUE, ignore.strand=FALSE)

## S4 method for signature 'RangedSummarizedExperiment'
promoters(x, upstream=2000, downstream=200)

## S4 method for signature 'RangedSummarizedExperiment'
restrict(x, start=NA, end=NA, keep.all.ranges=FALSE,
         use.names=TRUE)

## S4 method for signature 'RangedSummarizedExperiment'
trim(x, use.names=TRUE)

Arguments

Details

These transformations operate on the rowRanges component of the RangedSummarizedExperiment object, which can be a GenomicRanges or GRangesList object.

More precisely, any of the above functions performs the following transformation on RangedSummarizedExperiment object x:

    rowRanges(x) <- f(rowRanges(x), ...)

where f is the name of the function and ... any additional arguments passed to it.

See ?shift in the GenomicRanges package for the details of how these transformations operate on a GenomicRanges or GRangesList object.

See Also

• RangedSummarizedExperiment objects.

• The shift man page in the GenomicRanges package where intra range transformations of a GenomicRanges or GRangesList object are documented.

Examples

nrows <- 20; ncols <- 6
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
rowRanges <- GRanges(rep(c("chr1", "chr2"), c(5, 15)),
                     IRanges(sample(1000L, 20), width=100),
                     strand=Rle(c("+", "-"), c(12, 8)))
colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
                     row.names=LETTERS[1:6])
rse0 <- SummarizedExperiment(assays=SimpleList(counts=counts),
                             rowRanges=rowRanges, colData=colData)

rse1 <- shift(rse0, 1)
stopifnot(identical(
  rowRanges(rse1),
  shift(rowRanges(rse0), 1)
))

se2 <- narrow(rse0, start=10, end=-15)
stopifnot(identical(
  rowRanges(se2),
  narrow(rowRanges(rse0), start=10, end=-15)
))

se3 <- resize(rse0, width=75)
stopifnot(identical(
  rowRanges(se3),
  resize(rowRanges(rse0), width=75)
))

se4 <- flank(rse0, width=20)
stopifnot(identical(
  rowRanges(se4),
  flank(rowRanges(rse0), width=20)
))

se5 <- restrict(rse0, start=200, end=700, keep.all.ranges=TRUE)
stopifnot(identical(
  rowRanges(se5),
  restrict(rowRanges(rse0), start=200, end=700, keep.all.ranges=TRUE)
))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(SummarizedExperiment)
Loading required package: GenomicRanges
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, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SummarizedExperiment/intra-range-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: intra-range-methods
> ### Title: Intra range transformations of a RangedSummarizedExperiment
> ###   object
> ### Aliases: intra-range-methods shift
> ###   shift,RangedSummarizedExperiment-method narrow
> ###   narrow,RangedSummarizedExperiment-method resize
> ###   resize,RangedSummarizedExperiment-method flank
> ###   flank,RangedSummarizedExperiment-method promoters
> ###   promoters,RangedSummarizedExperiment-method restrict
> ###   restrict,RangedSummarizedExperiment-method
> ###   trim,RangedSummarizedExperiment-method
> ### Keywords: methods utilities
> 
> ### ** Examples
> 
> nrows <- 20; ncols <- 6
> counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
> rowRanges <- GRanges(rep(c("chr1", "chr2"), c(5, 15)),
+                      IRanges(sample(1000L, 20), width=100),
+                      strand=Rle(c("+", "-"), c(12, 8)))
> colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
+                      row.names=LETTERS[1:6])
> rse0 <- SummarizedExperiment(assays=SimpleList(counts=counts),
+                              rowRanges=rowRanges, colData=colData)
> 
> rse1 <- shift(rse0, 1)
> stopifnot(identical(
+   rowRanges(rse1),
+   shift(rowRanges(rse0), 1)
+ ))
> 
> se2 <- narrow(rse0, start=10, end=-15)
> stopifnot(identical(
+   rowRanges(se2),
+   narrow(rowRanges(rse0), start=10, end=-15)
+ ))
> 
> se3 <- resize(rse0, width=75)
> stopifnot(identical(
+   rowRanges(se3),
+   resize(rowRanges(rse0), width=75)
+ ))
> 
> se4 <- flank(rse0, width=20)
> stopifnot(identical(
+   rowRanges(se4),
+   flank(rowRanges(rse0), width=20)
+ ))
> 
> se5 <- restrict(rse0, start=200, end=700, keep.all.ranges=TRUE)
> stopifnot(identical(
+   rowRanges(se5),
+   restrict(rowRanges(rse0), start=200, end=700, keep.all.ranges=TRUE)
+ ))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>