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dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
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Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE. Traceback: #161

Open ArzooShamoon opened 2 months ago

ArzooShamoon commented 2 months ago

I tried to run singleR for cell type annotation to each cluster. head(Sample.combined) A data.frame: 10 × 6 orig.ident nCount_RNA nFeature_RNA percent.mt integrated_snn_res.0.5 seurat_clusters

MSC_AAACGAAAGAGAATCT-1 MSC 19477 4423 3.9533809 0 0 MSC_AAACGAAAGAGTCCGA-1 MSC 8237 3180 2.3188054 10 10 MSC_AAACGAACACAGCATT-1 MSC 4225 1859 7.3609467 4 4 MSC_AAACGCTCAAAGACGC-1 MSC 12958 3852 2.5158203 12 12 MSC_AAACGCTGTAACTAAG-1 MSC 874 294 0.5720824 1 1 MSC_AAAGAACGTACACTCA-1 MSC 6487 1351 1.0790812 1 1 MSC_AAAGGATTCTGTGCAA-1 MSC 1591 822 4.2740415 0 0 MSC_AAAGGGCAGCGTCAGA-1 MSC 27910 5472 3.2891437 0 0 MSC_AAAGGGCAGGAGAGGC-1 MSC 4829 995 0.5384138 9 9 MSC_AAAGGGCAGGTACCTT-1 MSC 18817 4437 2.4711697 0 0 ref <- celldex::HumanPrimaryCellAtlasData() colData(ref) results <- SingleR (test = as.SingleCellExperiment(Sample.combined), ref = ref, labels = ref$label.main) results **Error:** useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE. Traceback: 1. SingleR(test = as.SingleCellExperiment(Sample.combined), ref = ref, . labels = ref$label.main) 2. trainSingleR(ref, labels, genes = genes, sd.thresh = sd.thresh, . de.method = de.method, de.n = de.n, de.args = de.args, aggr.ref = aggr.ref, . aggr.args = aggr.args, recompute = recompute, restrict = restrict, . check.missing = FALSE, BNPARAM = BNPARAM, num.threads = num.threads, . BPPARAM = BPPARAM) 3. mapply(FUN = .identify_genes, ref = ref, labels = labels, genes = genes, . MoreArgs = list(de.method = de.method, de.n = de.n, de.args = de.args, . BPPARAM = BPPARAM), SIMPLIFY = FALSE) 4. (function (ref, labels, genes = "de", de.method = "classic", . de.n = NULL, de.args = list(), BPPARAM = BPPARAM) . { . if (length(labels) != ncol(ref)) { . stop("number of labels must be equal to number of cells") . } . if (.is_list(genes)) { . is.char <- vapply(genes, is.character, TRUE) . if (all(is.char)) { . genes <- .convert_per_label_set(genes) . } . else if (any(is.char)) { ... 14. matrixStats::rowMedians(x, rows = rows, cols = cols, na.rm = na.rm, . dim. = dim., ..., useNames = useNames) 15. deprecatedUseNamesNA() 16. .Defunct(msg = "useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.", . package = .packageName)
dviraran commented 2 months ago

This repo is not maintained. Please raise issues @ https://github.com/LTLA/SingleR