Add a read-level assay to a SummarizedExperiment object

Usage

addReadLevelAssay(
  se,
  assayDF,
  assayName,
  replaceExisting = FALSE,
  verbose = FALSE
)

Arguments

se: A SummarizedExperiment object.
assayDF: A DataFrame with the same dimensionality as se. Each column should be a read-level NaMatrix for a single sample.
assayName: A character scalar giving the name of the new assay.
replaceExisting: A logical scalar indicating whether to replace an existing assay with the same name or not.
verbose: Logical scalar. If TRUE, report on progress.

Value

A SummarizedExperiment object with the new read-level assay added.

Author

Charlotte Soneson

Examples

library(SummarizedExperiment)
#> Loading required package: MatrixGenerics
#> Loading required package: matrixStats
#> 
#> Attaching package: ‘MatrixGenerics’
#> The following objects are masked from ‘package:matrixStats’:
#> 
#>     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
#>     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
#>     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
#>     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
#>     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
#>     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
#>     colWeightedMeans, colWeightedMedians, colWeightedSds,
#>     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
#>     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
#>     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
#>     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
#>     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
#>     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
#>     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
#>     rowWeightedSds, rowWeightedVars
#> Loading required package: GenomicRanges
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#> Loading required package: generics
#> 
#> Attaching package: ‘generics’
#> The following objects are masked from ‘package:base’:
#> 
#>     as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
#>     setequal, union
#> 
#> Attaching package: ‘BiocGenerics’
#> 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, aperm, append,
#>     as.data.frame, basename, cbind, colnames, dirname, do.call,
#>     duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
#>     mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
#>     rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
#>     unsplit, which.max, which.min
#> Loading required package: S4Vectors
#> 
#> Attaching package: ‘S4Vectors’
#> The following object is masked from ‘package:utils’:
#> 
#>     findMatches
#> The following objects are masked from ‘package:base’:
#> 
#>     I, expand.grid, unname
#> Loading required package: IRanges
#> Loading required package: Seqinfo
#> 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")'.
#> 
#> Attaching package: ‘Biobase’
#> The following object is masked from ‘package:MatrixGenerics’:
#> 
#>     rowMedians
#> The following objects are masked from ‘package:matrixStats’:
#> 
#>     anyMissing, rowMedians
library(S4Vectors)
modbamfile <- system.file("extdata", "6mA_1_10reads.bam",
                          package = "SingleMoleculeGenomicsIO")
se <- readModBam(bamfiles = modbamfile, regions = "chr1:6940000-6955000",
                 modbase = "a", verbose = TRUE,
                 BPPARAM = BiocParallel::SerialParam())
#> ℹ extracting base modifications from modBAM files
#> ℹ finding unique genomic positions...
#> ✔ finding unique genomic positions... [47ms]
#> 
#> ℹ collapsed 11300 positions to 4772 unique ones
#> ✔ collapsed 11300 positions to 4772 unique ones [244ms]
#> 
# duplicate the 'mod_prob' assay into a new assay named 'new_assay'
se <- addReadLevelAssay(se, assayDF = assay(se, "mod_prob"),
                        assayName = "new_assay")
assayNames(se)
#> [1] "mod_prob"  "new_assay"
metadata(se)$readLevelData
#> $assayNames
#> [1] "mod_prob"  "new_assay"
#> 
#> $colDataColumns
#> [1] "readInfo"
#>