add calcN parameter to CreateSeuratObject

[mhkowalski]

I'm not 100% sure that we want to do this, but I am playing around with adding a calcN parameter to CreateSeuratObject to enable disabling/enabling the calculation of nCounts and nFeatures without overriding the global option. This would be cleaner for internal functions to enable specific behavior without having to carefully set/return global options.

If we want to do this, I'll write documentation and tests for this parameter.

devtools::load_all("~/data/github/seurat-object/")
devtools::load_all("~/data/github/seurat/")

getOption("Seurat.object.assay.calcn")

#global option is set to null by default
obj <- CreateSeuratObject(pbmc_small[['RNA']]$counts, 
                          calcN=FALSE)
grep("nCount_RNA", colnames(obj[[]]))
obj <- CreateSeuratObject(pbmc_small[['RNA']]$counts, 
                          calcN=TRUE)
grep("nCount_RNA", colnames(obj[[]]))
obj <- CreateSeuratObject(pbmc_small[['RNA']]$counts)
grep("nCount_RNA", colnames(obj[[]]))

#set global default but override if set in function call
options("Seurat.object.assay.calcn" = FALSE)
obj <- CreateSeuratObject(pbmc_small[['RNA']]$counts)
grep("nCount_RNA", colnames(obj[[]]))
obj <- CreateSeuratObject(pbmc_small[['RNA']]$counts, 
                          calcN=TRUE)
grep("nCount_RNA", colnames(obj[[]]))

[mojaveazure]

The options() approach was selected to allow internal functions to opt-out of running .CalcN(), while keeping it running for user-facing operations. An alternative to the op <- options(); on.exit(options(op)) would be using withr::with_options() or withr::local_options() in interal Seurat functions (withr has no dependencies and basically automates the op <- options(); on.exit(options(op)) construct), which I think would be better than exposing a calcN parameter