atRegions fails when given dropNA argument

[jamorrison]

When calling atRegions(bsseq, regions, mappings, nm, ...), you can pass it either dropNA or impute, which will then be passed on to summarizeBsSeqOver. When trying to pass it dropNA, atRegions will fail because of an incorrect number of dimensions (see error message below). The issue is arising because summarizeBsSeqOver will return a numeric, rather than a matrix, when only one sample is given. Should summarizeBsSeqOver always return a matrix, and then let atRegions reduce this to a numeric if there is only one sample?

Code:
tcga_bed <- system.file("extdata", "TCGA_BLCA_A13J_chr11p15_merged.bed.gz",
package = "biscuiteer")
tcga_vcf <- system.file("extdata", "TCGA_BLCA_A13J_header_only.vcf.gz",
package = "biscuiteer")
bisc <- read.biscuit(BEDfile = tcga_bed, VCFfile = tcga_vcf,
merged = TRUE, genome = "hg38", verbose = TRUE)

reg <- Ranges(seqnames = rep("chr11",5),
strand = rep("*",5),
ranges = IRanges(start = c(0,2.8e6,1.17e7,1.38e7,1.69e7),
end= c(2.8e6,1.17e7,1.38e7,1.69e7,2.2e7))
)
regions <- atRegions(bsseq = bisc, regions = reg, dropNA = TRUE)

Error message:
Error in regional[as.character(regions), ] :
incorrect number of dimensions