find_dupe_txis: Mark duplicated mcols(txis)$symbol in a SingleCellExperiment...

In trichelab/velocessor: The world's dumbest single-cell RNA velocity calculator and loader

Description

For large experiments, it may not be possible to run rowsum on a Matrix in limited memory. And, on occasion, it may not be necessary – if only one of the ENSEMBL gene IDs mapping to an HGNC or mouse symbol is nonzero, we don't need to sum them at all; dropping the near-zero rows is sufficient. This function allows looping through the ENSEMBL IDs for each "duplicated" symbol and determining whether rowsum() needs to be called at all.

Usage

find_dupe_txis(txis, mincount = 1, mincells = 1)

Arguments

txis	a SingleCellExperiment
mincount	minimum count to register as nonzero (1)
mincells	how many cells must have at least mincount to retain? (1)

Details

If there are no duplicated symbols, an empty data.frame results.

Value

       data.frame with symbol, ensembl, index, cutoff, cells

trichelab/velocessor documentation built on Jan. 5, 2022, 6:27 p.m.