Skip to contents

Create a GRanges from a SummarizedExperiment.

Source: R/scanGenome.R
getRangesWithAssayValues.Rd

Create a GRanges object from rowRanges and assay of a SummarizedExperiment object.

Usage

getRangesWithAssayValues(se, assayName)

Arguments

se

RangedSummarizedExperiment object, for example returned by quantifyWindowsInRegion.

assayName

Character scalar defining the assay to be extracted from se and set as mcols(...) of the return value. Thus, each column of the assay will become a column in mcols(...). If missing, the first assay from se will be used.

Value

A GRanges object, with the selected assay in its metadata columns.

Author

Charlotte Soneson, Michael Stadler

Examples

modbamfiles <- system.file("extdata",
                           c("6mA_1_10reads.bam", "6mA_1_10reads.bam",
                             "6mA_2_10reads.bam", "6mA_2_10reads.bam"),
                           package = "footprintR")
se <- quantifyWindowsInRegion(bamfiles = modbamfiles,
                              region = "chr1:6940000-6955000", modbase = "a",
                              BPPARAM = BiocParallel::SerialParam())
gr <- getRangesWithAssayValues(se, assayName = "Nmod")
gr
#> GRanges object with 136 ranges and 4 metadata columns:
#>       seqnames          ranges strand |   Nmod.s1   Nmod.s2   Nmod.s3   Nmod.s4
#>          <Rle>       <IRanges>  <Rle> | <numeric> <numeric> <numeric> <numeric>
#>     1     chr1 6940000-6940023      * |         0         0         6         6
#>     2     chr1 6940012-6940035      * |         0         0         8         8
#>     3     chr1 6940024-6940047      * |         0         0         3         3
#>     4     chr1 6940036-6940059      * |         2         2         1         1
#>     5     chr1 6940048-6940071      * |         2         2         2         2
#>   ...      ...             ...    ... .       ...       ...       ...       ...
#>   132     chr1 6941572-6941595      * |         0         0         0         0
#>   133     chr1 6941584-6941607      * |         0         0         0         0
#>   134     chr1 6941596-6941619      * |         0         0         0         0
#>   135     chr1 6941608-6941631      * |         0         0         0         0
#>   136     chr1 6941620-6941643      * |         0         0         0         0
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths