get_exprs: Generic accessor for expression data from an SCESet object.

In dynverse/scaterlegacy: Single-cell analysis toolkit for gene expression data in R

Description

Access by name a matrix of expression values, one row for each feature (gene, exon, region, etc), and one column for each cell stored an element of the assayData slot of the SCESet object.

Usage

get_exprs(object, exprs_values, ...)

## S4 method for signature 'SCESet'
get_exprs(object, exprs_values, warning = TRUE)

## S4 method for signature 'SCESet'
get_exprs(object, exprs_values = "exprs", warning = TRUE)

Arguments

object	a SCESet object.
exprs_values	character string indicating which values should be used as the expression values for this plot. Valid arguments are "tpm" (transcripts per million), "norm_tpm" (normalised TPM values), "fpkm" (FPKM values), "norm_fpkm" (normalised FPKM values), "counts" (counts for each feature), "norm_counts", "cpm" (counts-per-million), "norm_cpm" (normalised counts-per-million), "exprs" (whatever is in the 'exprs' slot of the SCESet object; default), "norm_exprs" (normalised expression values) or "stand_exprs" (standardised expression values) or any other slots that have been added to the "assayData" slot by the user.
...	further arguments passed to get_exprs.SCESet
warning	a logical scalar specifying whether a warning should be raised, and NULL returned, if the requested expression values are not present in object. Otherwise, an error will be thrown.

Value

a matrix of expression values

Author(s)

Davis McCarthy

Examples

data("sc_example_counts")
data("sc_example_cell_info")
example_sceset <- newSCESet(countData = sc_example_counts)
get_exprs(example_sceset, "counts")

## new slots can be defined and accessed
set_exprs(example_sceset, "scaled_counts") <- t(t(counts(example_sceset)) /
colSums(counts(example_sceset)))
get_exprs(example_sceset, "scaled_counts")[1:6, 1:6]

dynverse/scaterlegacy documentation built on Feb. 17, 2020, 5:07 a.m.