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I am currently running the SPOTlight package and attempting the spotlight decomposition portion of the. code on my reference scRNAseq data. The code I am running is below:

#Spotlight decomposition
set.seed(123)
spotlight_ls <-spotlight_deconvolution(
se_sc = E14_sc,
counts_spatial = anterior@assays$RNA@counts,
clust_vr = "subclass", # Variable in sc_seu containing the cell-type annotation
cluster_markers = cluster_markers_all, # Dataframe with the marker genes
cl_n = 100, # number of cells per cell type to use
hvg = 3000, # Number of HVG to use
ntop = NULL, # How many of the marker genes to use (by default all)
transf = "uv", # Perform unit-variance scaling per cell and spot prior to 
factorzation and NLS
method = "nsNMF", # Factorization method
min_cont = 0 # Remove those cells contributing to a spot below a certain threshold
)

When I run this code, I get the following error: Error in spotlight_deconvolution(se_sc = E14_sc, counts_spatial = anterior@assays$RNA@counts, : could not find function "spotlight_deconvolution"

ChristinaComo
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  • Here is my SessionInfo: version R version 4.1.2 (2021-11-01) os macOS Monterey 12.0.1 system x86_64, darwin17.0 ui RStudio language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz America/Denver date 2022-01-23 rstudio 2021.09.0+351 Ghost Orchid (desktop) pandoc 2.14.0.3 @ /Applications/RStudio.app/Contents/MacOS/pandoc/ (via rmarkdown) – ChristinaComo Jan 23 '22 at 21:58

1 Answers1

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I got the same error. The name of the function is just SPOTlight() now and the parameters names have been updated, but I think the function is the same.

mihika
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