label_cells: barebones cell labeling function

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

Description

Uses singleR to label celltypes. More sophisticated users may want to work directly with SingleR input and output for (e.g.) specific gene sets.

Usage

label_cells(
  txis,
  species = NULL,
  ret = c("sce", "labels"),
  downsample = NULL,
  maxcells = 10,
  mincells = 10,
  label = "label.main",
  ref = NULL,
  ...
)

Arguments

txis	a SingleCellExperiment
species	what species is this from? (autodetect Hs/Mm)
ret	what kind of object to return
downsample	downsample? (if ncol(txis) > 20000, TRUE, else FALSE)
maxcells	maximum number of cells per_sample per cluster (20)
mincells	minimum number of cells per cluster (10)
label	which label to use ("label.main")
ref	a reference SummarizedExperiment (default: HPCD/ImmGen)
...	other arguments passed to SingleR

Details

Autodetection of species will fail if the genome for the SingleCellExperiment does not contain "GRCm", "mm", "GRCh", or "hg". Once reasonable reference datasets are available for GRCz/dr genomes, we will support those too.

Twenty cells per sample per cluster may be an awful lot of cells if you have a large number of samples (i.e. GEMcode preps). Setting maxcells as low as 10, or perhaps even lower (see upcoming cluster-by-sample plots), if the cells comprising a cluster come from across many samples. The quick way to find this out is with a plot,

Value

depending on the value of 'ret', either an SCE or a set of labels

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