we recommend to only merge simulations from the same dataset object, otherwise the count matrices might not correspond on the gene level
Value
named list; bulk a SummarizedExperiment object, where the assays store the simulated bulk RNAseq datasets. Can hold either one or two assays, depending on how many matrices were present in the dataset
cell-fractions is a dataframe with the simulated cell-fractions per sample;
scaling_vector scaling value for each cell in dataset
Examples
counts <- Matrix::Matrix(matrix(rpois(3e5, 5), ncol=300), sparse = TRUE)
#> Error in rpois(3e+05, 5): could not find function "rpois"
tpm <- Matrix::Matrix(matrix(rpois(3e5, 5), ncol=300), sparse = TRUE)
#> Error in rpois(3e+05, 5): could not find function "rpois"
tpm <- Matrix::t(1e6*Matrix::t(tpm)/Matrix::colSums(tpm))
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 't': error in evaluating the argument 'x' in selecting a method for function 't': object 'tpm' not found
colnames(counts) <- paste0("cell_",rep(1:300))
#> Error in colnames(counts) <- paste0("cell_", rep(1:300)): object 'counts' not found
colnames(tpm) <- paste0("cell_",rep(1:300))
#> Error in colnames(tpm) <- paste0("cell_", rep(1:300)): object 'tpm' not found
rownames(counts) <- paste0("gene_",rep(1:1000))
#> Error in rownames(counts) <- paste0("gene_", rep(1:1000)): object 'counts' not found
rownames(tpm) <- paste0("gene_",rep(1:1000))
#> Error in rownames(tpm) <- paste0("gene_", rep(1:1000)): object 'tpm' not found
annotation <- data.frame("ID"=paste0("cell_",rep(1:300)),
"cell_type"=c(rep("T cells CD4",50),
rep("T cells CD8",50),
rep("Macrophages",100),
rep("NK cells",10),
rep("B cells",70),
rep("Monocytes",20)))
dataset <- SimBu::dataset(annotation = annotation,
count_matrix = counts,
tpm_matrix = tpm,
name = "test_dataset")
#> Error in generate_summarized_experiment(annotation = annotation, count_matrix = count_matrix, tpm_matrix = tpm_matrix, name = name, spike_in_col = spike_in_col, additional_cols = additional_cols, filter_genes = filter_genes, variance_cutoff = variance_cutoff, type_abundance_cutoff = type_abundance_cutoff, scale_tpm = scale_tpm): object 'counts' not found
s1 <- SimBu::simulate_bulk(dataset,
scenario="even",
scaling_factor="NONE",
nsamples=10,
ncells=100)
#> Error in (function (classes, fdef, mtable) { methods <- .findInheritedMethods(classes, fdef, mtable) if (length(methods) == 1L) return(methods[[1L]]) else if (length(methods) == 0L) { cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ") stop(gettextf("unable to find an inherited method for function %s for signature %s", sQuote(fdef@generic), sQuote(cnames)), domain = NA) } else stop("Internal error in finding inherited methods; didn't return a unique method", domain = NA)})(list("function"), new("standardGeneric", .Data = function (x, ...) standardGeneric("colData"), generic = structure("colData", package = "SummarizedExperiment"), package = "SummarizedExperiment", group = list(), valueClass = character(0), signature = "x", default = NULL, skeleton = (function (x, ...) stop("invalid call in method dispatch to 'colData' (no default method)", domain = NA))(x, ...)), <environment>): unable to find an inherited method for function ‘colData’ for signature ‘"function"’
s2 <- SimBu::simulate_bulk(dataset,
scenario="even",
scaling_factor="NONE",
nsamples=10,
ncells=100)
#> Error in (function (classes, fdef, mtable) { methods <- .findInheritedMethods(classes, fdef, mtable) if (length(methods) == 1L) return(methods[[1L]]) else if (length(methods) == 0L) { cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ") stop(gettextf("unable to find an inherited method for function %s for signature %s", sQuote(fdef@generic), sQuote(cnames)), domain = NA) } else stop("Internal error in finding inherited methods; didn't return a unique method", domain = NA)})(list("function"), new("standardGeneric", .Data = function (x, ...) standardGeneric("colData"), generic = structure("colData", package = "SummarizedExperiment"), package = "SummarizedExperiment", group = list(), valueClass = character(0), signature = "x", default = NULL, skeleton = (function (x, ...) stop("invalid call in method dispatch to 'colData' (no default method)", domain = NA))(x, ...)), <environment>): unable to find an inherited method for function ‘colData’ for signature ‘"function"’
s <- SimBu::merge_simulations(list(s1,s2))
#> Error in SimBu::merge_simulations(list(s1, s2)): object 's1' not found