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

Description Usage Arguments Value Examples

View source: R/calculate-expression.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

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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

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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")

scater documentation built on May 31, 2017, 3:08 p.m.

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