prepSCE | R Documentation |
...
prepSCE( x, kid = "cluster_id", sid = "sample_id", gid = "group_id", drop = FALSE )
x |
a SingleCellExperiment. |
kid, sid, gid |
character strings specifying
the |
drop |
logical. Specifies whether |
a SingleCellExperiment.
Helena L Crowell
# generate random counts ng <- 50 nc <- 200 # generate some cell metadata gids <- sample(c("groupA", "groupB"), nc, TRUE) sids <- sample(paste0("sample", seq_len(3)), nc, TRUE) kids <- sample(paste0("cluster", seq_len(5)), nc, TRUE) batch <- sample(seq_len(3), nc, TRUE) cd <- data.frame(group = gids, id = sids, cluster = kids, batch) # construct SCE library(scuttle) sce <- mockSCE(ncells = nc, ngenes = ng) colData(sce) <- cbind(colData(sce), cd) # prep. for workflow sce <- prepSCE(sce, kid = "cluster", sid = "id", gid = "group") head(colData(sce)) metadata(sce)$experiment_info sce
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