accessors: Additional accessors for the typical elements of a...

In scater: Single-Cell Analysis Toolkit for Gene Expression Data in R

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

example_sce <- mockSCE()
example_sce <- logNormCounts(example_sce)
head(logcounts(example_sce)[,1:10])
head(exprs(example_sce)[,1:10]) # identical to logcounts()

norm_exprs(example_sce) <- log2(calculateCPM(example_sce) + 1)

stand_exprs(example_sce) <- log2(calculateCPM(example_sce) + 1)

tpm(example_sce) <- calculateTPM(example_sce, lengths = 5e4)

cpm(example_sce) <- calculateCPM(example_sce)

fpkm(example_sce)

scater documentation built on Feb. 28, 2021, 2:01 a.m.