norm_exprs {scater} | R Documentation |
Convenience functions to access commonly-used assays of the
SingleCellExperiment
object.
norm_exprs(object) norm_exprs(object) <- value stand_exprs(object) stand_exprs(object) <- value fpkm(object) fpkm(object) <- value
object |
|
value |
a numeric matrix (e.g. for |
a matrix of normalised expression data
a matrix of standardised expressiond data
a matrix of FPKM values
A matrix of numeric, integer or logical values.
Davis McCarthy
data("sc_example_counts") data("sc_example_cell_info") example_sce <- SingleCellExperiment( assays = list(counts = sc_example_counts), colData = sc_example_cell_info) example_sce <- normalize(example_sce) head(logcounts(example_sce)[,1:10]) head(exprs(example_sce)[,1:10]) # identical to logcounts() example_sce <- SingleCellExperiment( assays = list(norm_counts = sc_example_counts), colData = sc_example_cell_info) counts(example_sce) <- sc_example_counts norm_exprs(example_sce) <- log2(calculateCPM(example_sce, use_size_factors = FALSE) + 1) stand_exprs(example_sce) <- log2(calculateCPM(example_sce, use_size_factors = FALSE) + 1) tpm(example_sce) <- calculateTPM(example_sce, effective_length = 5e4) cpm(example_sce) <- calculateCPM(example_sce, use_size_factors = FALSE) fpkm(example_sce)