bsgenome objects

[nsheff]

in this scripts/installRdeps.R you are downloading and installing gigabytes of bsgenome objects.

bedstat/scripts/installRdeps.R

Lines 15 to 23 in bd90e7c

	genomes = list(Hsapiens = c("hg18","hg19","hg38"),
	Mmusculus = c("mm10","mm9"))
	for(name in names(genomes)) {
	for(genome in genomes[[name]]) {
	# should install non-masked too
	.install_pkg(p=paste0("BSgenome.", name,
	".UCSC.", genome,".masked"),
	bioc=TRUE)
	}

[nsheff]

The problem is: I may not even want these genomes. So...

1. the gc content calculation in bedstat should be optional, or should see if you have the correct object installed or something.

2. the tutorial should not force you to download all this data for all these genomes. it could be an optional step? further, the tutorial doesn't even use all of these, so it should only even offer as an option to download the ones it actually uses.

3. perhaps we should see if there's a way to do a gc content calc without these objects.