calcIsExprs: Calculate which features are expressed in which cells using a...

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

Description

Calculate which features are expressed in which cells using a threshold on observed counts, transcripts-per-million, counts-per-million, FPKM, or defined expression levels.

Usage

calcIsExprs(object, lowerDetectionLimit = NULL, exprs_values = NULL)

Arguments

object	an SCESet object with expression and/or count data.
lowerDetectionLimit	numeric scalar giving the minimum expression level for an expression observation in a cell for it to qualify as expressed.
exprs_values	character scalar indicating whether the count data ("counts"), the transformed expression data ("exprs"), transcript-per-million ("tpm"), counts-per-million ("cpm") or FPKM ("fpkm") should be used to define if an observation is expressed or not. Defaults to the first available value of those options in the order shown.

Value

a logical matrix indicating whether or not a feature in a particular cell is expressed.

Examples

data("sc_example_counts")
data("sc_example_cell_info")
example_sceset <- newSCESet(countData=sc_example_counts)
is_exprs(example_sceset) <- calcIsExprs(example_sceset, lowerDetectionLimit = 1,
exprs_values = "exprs")

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