martijnvanattekum / cleanse Goto Github PK

Hi @martijnvanattekum,

I saw cleanse submitted to Bioconductor and it prompted me to take a quick look at the package.

This is just a comment on something that caught my eye in the README.md, and this is partly a matter of perhaps personal coding style, but an example of 'native syntax' struck me as a bit 'non-native'/'unnatural' (for want of a better word):

# From README.md: "Using native syntax"
coldata <- colData(se) 
indices <- which(coldata$time == 4) 
se[,indices] 

I think most 'base R-centric Bioconductor' users would use the simpler:

se[, which(se$time == 4)]

Or, if you know there are no NAs, then the even simpler:

se[, se$time == 4]

Anyway, it's a minor thing, but when comparing 'base' vs. 'tidy' approaches I think it pays to try to write both versions as 'natively'/'naturally' as possible.

Cheers,
Pete