remove_TEC_doublets: Remove intra-TEC doublets by finding cells with both a high...
In maehrlab/thymusatlastools: Tools for analysis of single-cell transcriptomic data

Description Usage Arguments Details Value

Remove intra-TEC doublets by finding cells with both a high cTEC signature and a high mTEC signature.

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remove_TEC_doublets(dge, results_path, mTEC_thresh = NULL,
  cTEC_thresh = NULL, pure_fraction_mTEC = 0.02, pure_fraction_cTEC = 0.2,
  reject_rate = 0.05)

`dge`	Seurat object
`results_path`	Plots are saved here.
`mTEC_thresh,`	@param cTEC_thresh Cells are excluded if they exceed both thresholds. If these are NULL, they are selected automatically.

For threshold selection, we isolate some nearly-pure cTECs by ranking with all cells on cTEC signatures and retaining the top pure_fraction_cTEC (default 20 Among those cells, we take the (1 - reject_rate) quantile (default 98th percentile), as the rejection threshold. The same process is used for mTEC threshold selection, but pure_fraction_mTEC defaults to just 2

A list with names "dge", "mTEC_thresh", and "cTEC_thresh."

maehrlab/thymusatlastools documentation built on May 28, 2019, 2:32 a.m.