scater (version 1.0.4)

calcIsExprs: 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.

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_data = "counts")

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_data

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.

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_data = "exprs")