subset() function does not respect the order of indices

[dolchan]

subset() function does not seem to respect the order of indices. For example, spe[c(2,1), ] will return the same result as subset[c(1,2), ]. The same goes with spe[, 1:2] and spe[, c(2,1)]. I am not sure if this is by design or a bug, but it is not intuitive and is not consistent with what's expected. When I tested it with SingleCellExperiment, sce[1:2, ] is different from sce[c(2,1), ]. This means there is no efficient way of permuting rows (genes) or columns (cells) in Seurat object.