Check internal consistency of SummarizedExperiment object

All assays with read-level data must have the same number and order of the reads, which must also agree with the order in se$QC if that exists. All assays must have the same column names, which must also agree with the column names of the object, and the sample column in the colData.

Usage

checkSEValidity(se, verbose = FALSE)

Arguments

se

A SummarizedExperiment object.

verbose

A logical scalar. If TRUE, report on progress.

Value

Silently returns NULL. If the object is not valid, an error will be raised.

Author

Charlotte Soneson

Examples

library(GenomicRanges)
modbamfiles <- system.file("extdata", c("6mA_1_10reads.bam",
                                        "6mA_2_10reads.bam"),
                           package = "SingleMoleculeGenomicsIO")
se <- readModBam(bamfiles = modbamfiles, regions = "chr1:6940000-6955000",
                 modbase = "a", verbose = FALSE,
                 variantPositions = GPos(seqnames = "chr1",
                                         pos = c(6940000, 6940500)),
                 BPPARAM = BiocParallel::SerialParam())
checkSEValidity(se)