Error with annotateCellTypesGSEA function

[odunola26]

Hello,

Please, I am trying to annotate my cells using the GSEA function with I list I generated myself as seen below, but it is throwing errors: Error in gset[[celltype]]$character : $ operator is invalid for atomic vectors

Could you please advise on how I can fix this problem?

Create a nested list cell_genes <- list(

Macrophages = c("PTPRC", "CD163", "MSR1", "CD14", "CD68", "AIF1", "CSF1R", "CD69", "APOC1"), Monocytes = c("PTPRC", "CD14", "FCGR3A", "FCGR3B", "TIMP1", "CD44", "G0S2"), NK_cells = c("PTPRC", "KLRK1", "NCR1"), Dendritic_cells = c("PTPRC", "CD1A", "HLA-DRA", "HLA-DRB1", "CD80", "CD86"), B_cells = c("PTPRC", "MS4A1", "CD19", "CD79A", "CD79B", "CD52", "BANK1", "IGHD", "IGHM", "CD69", "CD83"), CD4_T_cells = c("PTPRC", "CD3D", "CD3E", "CD3G", "CD4", "IL2RA", "CD28", "FOXP3"), CD8_T_cells = c("PTPRC", "CD3D", "CD3E", "CD3G", "CD8A", "CD8B", "GZMA", "GZMB", "PRF1"), Treg = c("FOXP3", "CD25", "CTLA4", "IL2RA", "IKZF2", "IKZF4"), Endothelial_cells = c("PECAM1", "FLT1", "PTPRB", "EGFL7", "VWF", "CDH5"), Skeletal_cells = c("MYOD1", "MYOG", "DES", "ACTA1", "MYH3"), Fibroblasts = c("ACTA2", "COL1A1", "COL1A2", "FAP", "PDGFRA", "PDGFRB"), Adipocytes = c("FABP4", "LEP", "ADIPOQ", "PPARG", "PLIN1"), HSC = c("HPCA1", "PROM1", "KIT", "THY1", "ENG"), Epithelial_cells = c("EPCAM", "KRT8", "KRT18", "CDH1", "MUC1") ) Perform annotation celltype_annotations <- annotateCellTypesGSEA(beta = gexp, gset = cell_genes, qval = 0.05)

Error in gset[[celltype]]$character : $ operator is invalid for atomic vectors

Thank you.

Regards, Odunola