Run AUCell classification

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

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.

See also

AUCell_calcAUC

Author

Nicholas Mikolajewicz

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)
#> Error in withCallingHandlers(expr, warning = function(w) if (inherits(w,     classes)) tryInvokeRestart("muffleWarning")): object 'so.query' not found
v.auc$plot.auc
#> Error in eval(expr, envir, enclos): object 'v.auc' not found
v.auc$plot.nm
#> Error in eval(expr, envir, enclos): object 'v.auc' not found
v.auc$plot.max.score
#> Error in eval(expr, envir, enclos): object 'v.auc' not found

g.auc <- runAUC(object = so.query, genelist = gsc.list, n.workers = 12)
#> Error in withCallingHandlers(expr, warning = function(w) if (inherits(w,     classes)) tryInvokeRestart("muffleWarning")): object 'so.query' not found
g.auc$plot.auc
#> Error in eval(expr, envir, enclos): object 'g.auc' not found
g.auc$plot.nm
#> Error in eval(expr, envir, enclos): object 'g.auc' not found
g.auc$plot.max.score
#> Error in eval(expr, envir, enclos): object 'g.auc' not found

n.auc <- runAUC(object = so.query, genelist = neftel.list, n.workers = 12)
#> Error in withCallingHandlers(expr, warning = function(w) if (inherits(w,     classes)) tryInvokeRestart("muffleWarning")): object 'so.query' not found
n.auc$plot.auc
#> Error in eval(expr, envir, enclos): object 'n.auc' not found
n.auc$plot.nm
#> Error in eval(expr, envir, enclos): object 'n.auc' not found
n.auc$plot.max.score
#> Error in eval(expr, envir, enclos): object 'n.auc' not found