runAUC: Run AUCell classification

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Run AUCell classification

Description

Run AUCell classification to identify active genesets in scRNAseq sample. Wrapper for AUCell package.

Usage

runAUC(
  object,
  genelist,
  assay = DefaultAssay(object),
  n.workers = 1,
  n.repeats = 5,
  n.iterations = 1000,
  posterior.p = 0.9,
  mixture.analysis = T,
  size = autoPointSize(ncol(object)),
  reduction = "umap",
  ...
)

Arguments

object	Seurat object
genelist	Named list of genesets.
assay	Assay used for expression matrix.
n.workers	Number of workers for parallelized implementation. Default is 1.
n.repeats	Number of fitting repeats (best fit taken). Default is 5.
n.iterations	Number of fitting iterations per a repeat. Default is 1000.
posterior.p	Posterior distribution membership threshold. Default is 0.9 (e.g., p > 0.9 is member).
mixture.analysis	logical to perform mixture analysis. Default = T (computationally intensive).
size	UMAP point size.
reduction	reduction used for visualization. Default is "umap".
...	additional parameters passed to geom_point(...)

Value

list of results along with ggplot handles visualizing class predictions overlaid on UMAP.

Author(s)

Nicholas Mikolajewicz

See Also

AUCell_calcAUC

Examples

# get genesets
verhaak.df <- geneSets[["Verhaak_CancerCell_2010"]]
verhaak.list <- wideDF2namedList(verhaak.df)

gsc.df <- geneSets[["Richards_NatureCancer_2021_sc"]]
gsc.list <- wideDF2namedList(gsc.df)

neftel.df <- geneSets[["GBM_Hs_Neftel2019"]]
neftel.list <- wideDF2namedList(neftel.df)

verhaak.list <- lapply(verhaak.list, toupper)
gsc.list <- lapply(gsc.list, toupper)
neftel.list <- lapply(neftel.list, toupper)

# classify cells based on provided genesets
v.auc <- runAUC(object = so.query, genelist = verhaak.list, n.workers = 12)
v.auc$plot.auc
v.auc$plot.nm
v.auc$plot.max.score

g.auc <- runAUC(object = so.query, genelist = gsc.list, n.workers = 12)
g.auc$plot.auc
g.auc$plot.nm
g.auc$plot.max.score

n.auc <- runAUC(object = so.query, genelist = neftel.list, n.workers = 12)
n.auc$plot.auc
n.auc$plot.nm
n.auc$plot.max.score

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.