norm_exprs {scater}R Documentation

Additional accessors for the typical elements of a SingleCellExperiment object.

Description

Convenience functions to access commonly-used assays of the SingleCellExperiment object.

Usage

norm_exprs(object)

norm_exprs(object) <- value

stand_exprs(object)

stand_exprs(object) <- value

fpkm(object)

fpkm(object) <- value

Arguments

object

SingleCellExperiment class object from which to access or to which to assign assay values. Namely: "exprs", norm_exprs", "stand_exprs", "fpkm". The following are imported from SingleCellExperiment: "counts", "normcounts", "logcounts", "cpm", "tpm".

value

a numeric matrix (e.g. for exprs)

Value

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.

Author(s)

Davis McCarthy

Examples

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)
[Package scater version 1.10.1 Index]