Should zero count genes filtering by optional

[jsleight1]

There are several pre-filtering approaches that can be used in RNAseq count data analysis:

• Filter genes with zero counts across all samples
• Filter genes that have sum(reads) < threshold across all samples
• Filter genes that have CPM < threshold across given number of samples
• More complex approaches such as those outlined by the function filterByExpr in the edgeR R package (https://f1000research.com/articles/5-1438)

I have noticed that the between sample normalisation methods in rnanorm automatically remove genes with zero counts across all samples. However would it be possible for this to be optionally, allowing the user to perform custom count filtering prior to passing to rnanorm's TMM normalisation for example.