find_eligible_cells: Find cells that meet certain cluster-wise criteria

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

Description

By default, to be eligible, a cell must come from a sample whose presence in a cluster appears to be non-noise (i.e. not the "soup" part of a mixture), and after pruning out samples that are all-one-cluster (likely artifacts) as well as clusters that are all-one-sample (likely artifacts), the cluster from which the cells come must have at least mincells cells left in it. The default for mincells is 10, so this isn't as harsh as it might seem, but it's not something you want to be relying upon for SmartSeq-like runs. One useful application of find_eligible_cells is to feed plot_eligible_cells, which can help determine whether to raise or lower maxcells and mincells in downsample_txis and label_cells.

Usage

find_eligible_cells(txis, mincells = 10)

Arguments

txis	SingleCellExperiment where !is.null(colLabels(txis))
mincells	min cells per cluster per sample (see Details) (10)

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