modify max pb # of samples

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R/deg.R

@@ -142,7 +142,7 @@ deg.prepare <- function(se, pathology, case, control, sample.col, filter_only_ca
     colnames(SummarizedExperiment::rowData(se))[colnames(SummarizedExperiment::rowData(se))=="strand"] = "Strand"
     pb = calculate_qc_metrics(se_make_pseudobulk(se, sample.col), assay="counts", qc_vars=c("mt", "ribo", "pc", "chrX", "chrY"))
     cat("Pseudobulk: ", ncol(pb), " samples\n")
-    stopifnot(S4Vectors::ncol(pb) <= 1000) ### we can't have uber-large sample numbers
+    stopifnot(S4Vectors::ncol(pb) <= 10000) ### we can't have uber-large sample numbers
     if (any(SummarizedExperiment::colData(pb)$total_counts < min.total.counts.per.sample)) {
         cd = SummarizedExperiment::colData(pb)
         cat("Bad samples:", rownames(cd)[cd$total_counts < min.total.counts.per.sample], "\n")