prepSCE {muscat} | R Documentation |
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prepSCE( x, kid = "cluster_id", sid = "sample_id", gid = "group_id", drop = FALSE )
x |
|
kid, sid, gid |
character strings specifying
the |
drop |
logical. Specifies whether |
Helena L Crowell
# generate random counts ng <- 50 nc <- 200 counts <- matrix(sample(ng * nc), nrow = ng, ncol = nc) # 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) # construct SCE library(SingleCellExperiment) sce <- SingleCellExperiment( assays = list(counts = counts), colData = data.frame(group = gids, id = sids, cluster = kids, batch)) # prep. for workflow sce <- prepSCE(sce, kid = "cluster", sid = "id", gid = "group") head(colData(sce)) metadata(sce)$experiment_info