Help figuring out what part of my object is throwing the subscript out of bounds error

[JasperGattiker]

Hello again. When running the initial celltalk function, I encounter the following error: .subscript.2ary(x, i, j, drop = TRUE) : subscript out of bounds. I've included the traceback below. This error occurs whether the scaled/normalized RNA assay is structures as a V5 or V3/4 Seurat assay. Has anyone else encountered this, and what did you do to fix it? Looking at the traceback, I can't figure out what to start troubleshooting.

celltalk(input_object=Integrated_DF, metadata_grouping="CellTypes_Assigned", ligand_receptor_pairs=ramilowski_pairs, number_cells_required=100, min_expression=1000, max_expression=20000, scramble_times=10)

Error in .subscript.2ary(x, i, j, drop = TRUE) : subscript out of bounds

traceback() 13: stop("subscript out of bounds") 12: .subscript.2ary(x, i, j, drop = TRUE) 11: methods::slot(object = object, name = layer)[features, cells] 10: methods::slot(object = object, name = layer)[features, cells] 9: LayerData.Assay(object = object, layer = layer) 8: LayerData(object = object, layer = layer) 7: .CalcN.Assay(object = x[[assay]]) 6: CalcN(object = x[[assay]]) 5: subset.Seurat(x = x, features = i, cells = j, ...) 4: [.Seurat(input_filtered, names(ligs.keep), ) 3: input_filtered[names(ligs.keep), ] 2: create_expression_matrices(input_object, metadata_grouping, ligand_receptor_pairs, number_cells_required, min_expression, max_expression) 1: celltalk(input_object = Integrated_DF, metadata_grouping = "CellTypes_Assigned", ligand_receptor_pairs = ramilowski_pairs, number_cells_required = 10, min_expression = 1000, max_expression = 20000, scramble_times = 10)