Bugfix to CellsByIdentities

[bbimber]

I think this is broken, at least in some R versions. If your object has more than one cell with NA as the ident you get an error like:

Warning message:
In cells.idents["NA"] <- names(x = which(x = is.na(x = Idents(object = object)[cells]))) :
number of items to replace is not a multiple of replacement length

You can repro this with the following:

library(Seurat)

dat <- matrix(1:100, ncol = 10, dimnames = list(LETTERS[1:10], LETTERS[11:20]))
df <- data.frame(x = LETTERS[5:14], field <- factor(c(rep('AA', 5), rep('BB', 5))), row.names = LETTERS[11:20])
so <- Seurat::CreateSeuratObject(dat, meta.data = df)

# Set NAs. These are cells N and O:
so@meta.data$field[4:5] <- NA
Idents(so) <- 'field'
Idents(so)

# This vector has two cells with NAs. If you have a single NA cell it will work:
cells <- c('M', 'N', 'O')
x <- Seurat::CellsByIdentities(
  object = so,
  idents = NULL,
  cells = cells
)

The problem is that R assignment with a single bracket fails when you're trying to assign a vector (hence why you need two or more NA cells).

[mojaveazure]

Thanks for catching and fixing this!